In Ao No Fuuin, Akira tortures an Oni child (about 4 years old in appearance, though it is implied to have been born only a few months ago) by draining its energy off and on while trying to gain information out of it. He says he'll even kill her if she won't answer soon enough.
Ladd Russo in Baccano! shoots a kid in the face with a shotgun for the hell of it. Vino also tortures said child, though since he had just watched Ladd shoot him in the face, he knew it wouldn't stick. And Czes had tried to get Ladd to kill everyone, so in Vino's mind he deserved it.
Berserk: To all Apostles, humans are food, toys or a combination of both. Children? They eat babies so...
Guts himself, at one point before fighting Rosine, had to take on her whole army of elves which was constituted of... young children she had previously kidnapped, brainwashed, and turned into monsters. Plus his actual fight against Rosine herself (who's no older than 12), or that he used a still-human child as bait for those monster elves.
Big Bad Griffith trumps everyone in that he not only raped his pregnant former commander Casca while in his demonic form, inadvertently poisoning the kid with his demonic seed but he also uses the child, who was since miscarried as a misshapen fetus but has thrived, during the mock eclipse as a vessel to reincarnate himself into the real world.
In Black Lagoon, Balalaika will come down like the wrath of God on anyone who dares to torture and kill her men. Even if they happen to be children. Doesn't mean she has to like it, though.
In the anime, a flashback to the Afghan war shows her shifting her sniper fire away from a child running towards its mother. So this trope is in effect, but not to a ridiculous degree — presumably she'd have no qualms about killing a Child Soldier, but it wouldn't be the same with a civilian child.
Revy herself is not above hurting kids either, though she usually has to be provoked into it. As Dutch says when he orders Rock to take over watching Garcia from a pissed-off Revy, "not a lot of maternal instinct there."
Hollows are driven by desperate hunger to kill humans beginning with their closest family and then encompassing anyone: man, woman or child. The most heinous example was Shrieker who was so evil he was a serial killer before he became a hollow. Grand Fisher, Numb Chandelier and Nnoitra are other notable examples.
Wonderweiss caused a few problems among the shinigami because of his young age. Kyouraku attacked him after he stabbed Ukitake, Kensei stated he was the kind of guy would take out a child if he had to protect someone and, while Yamamoto was relieved when Wonderweiss entered Super Mode because he no longer resembled a child, he hadn't hesitated to try and kill him while he still resembled one.
Yhwach carried out The Purge against all Gemischt. He killed countless men, women and children. The only survivor in history was Uryuu, who was eight years old when he mysteriously survived Yhwach's attempt to kill him.
BG9 will target anyone if he decides it'll benefit his ability to achieve his goals. He impales Omaeda's little sister in an attempt to force Omaeda to reveal the location of his captain.
Yuzu fell victim to an enemy who was willing to kill her to achieve his goal of opposing Ichigo. Kokuto, in fact.
The Homunculi of Busou Renkin liked to eat children, as their meat was more tender than adults. Tokiko was the only survivor of a homunculus attack on her grade school when she was 10.
Catnapped!: Princess Buburina attempts to turn both Meeko and her brother Toriyasu into balloons and pop them only to find that it doesn't work since they're both human. With the former, she tries to do it in retaliation forcalling her a witch, but when she finds that she can't pop her, she instead decides to turn her into a monster the next day, and with the latter, she tries to do so in order to stop him and Chu Chu from retrieving Papadoll... Guess what happens next?
It's worth noting that Doh Doh points out that Buburina is merciful to little kids, which might make sense considering she didn't try to kill Meeko until the latter insulted her not to mention that she and Toriyasu were both interfering with her plans for world domination. So it's likely that she wouldn't do this to a child unless they did something to make her angry, although it could've just been something Doh Doh said to urge Meeko to apologize.
In Bungou Stray Dogs, one of the Guild's plans centers on this. Steinbeck tortures Q, who's thirteen but looks and acts a bit younger, in order to make use of his ability to wreak havoc on Yokohama. On that note, Q's ability relies on his enemies not being above hurting him.
Code Geass has both sides slaughtering kids either off-screen or onscreen. On one hand, the Britannian Army kills Japanese/Eleven of all ages during the first episode's raid and the Euphinator Incident. On the other, episode 14 of R2 has Lelouch and his group doing likewise in the Geass Cult Massacre, since many of the Cult members are very young Tyke Bombs.
During the Ghost of Mater arc of D.Gray-Man, the Ghost had killed five humans that had attacked it when asked if they wanted to hear a song. It was ready to kill the sixth human child if it did the same as the others and didn't accept it.
Many cases in Detective Conan involve children getting hurt or killed by Asshole Victims. I.e., we have two schoolteachers strangling a girl no older than 12 to death because She Knows Too Much and then making it look like suicide; another case has Conan and his friends being chased around by a Serial Killer in a library during the night.
In Devilman, Amon doesn't care who is in his path. Child, baby... It's all good as long as it bleeds!
And so do his enemies, to be honest. Poor little Sachiko and Miki's younger brother.
Mild case of this in Digimon Tamers. Yamaki, in his desperation to stop the Digimon who keep coming into the real world, physically attacks main character Jen/Henry who is 10 in the Japanese version and 12 in the dub. Unlike most examples on this page, Yamaki eventually becomes The Atoner.
In Elfen Lied, Bandou has no qualms about hitting and maiming little girls. Lucy herself murders a bunch. Some were horrible bastards. Others weren't. Kurama would qualify too, for he is tasked with euthanizing diclonius newborns. And then we have the utterly depraved and horrendous stuff The Unknown Man does...
Agon of Eyeshield 21 threw a football at the knees of a kid in a wheelchair, thus cementing his status as the series' "villain" (or closest they have).
Many of Fist of the North Star's bad guys are not above visiting cruelty or worse upon children, and some of the worst, such as Jackal and Souther, have actually killed kids in the manga. Because Kenshiro is a Friend to All Children, his wrath is especially violent when these kinds of villains go too far.
Envy disguised as an officer deliberately killed an Ishbalan child, starting the Ishbalan Massacre.
In the 2003 anime version, Bradley/Pride kills his own son by breaking his neck. In this continuity, Selim is actually a normal kid and his real son.
In the same anime no one seems to mind beating Wrath around. He resembles a 8 - 10 year old child, tops.
In Fushigi Yuugi, Miboshi's ability is the ability to possess someone's body. He states that he prefers to possess children, because their innocent souls and small bodies make it easier to overtake them. His known victims include an unnamed young Buddhist monk (or monk-in-training), and Chiriko.
UryuuMinene plants bombs all over a school full of kids, and winds up killing quite a few of them.
Once he loses it, Yuki uses Kamado's orphans to lure John Balks and joins Yuno in killing them. Yes, you read that right. Though Yuki did believe he could bring them all back to life once he won the game and became God, and was planning to. Unfortunately, it turned out God cannot bring back the dead.
In Ginga Densetsu Weed, Thunder and Lector, the Doberman Pinscher assassins for Hougen, threaten to kill Teru if his father didn't kill Kyoshiro. It was also kinda personal, since Kyoshiro was the one who tore off Teru's father's ear.
In Guardian Fairy Michel, Salome and her gang are constantly at war with Kim and Michel. Aside from trying to harm or kill them, they've also kidnapped and attacked other children—or used the threat of doing so to make the heroes back off.
Umineko predecessor, Higurashi: When They Cry, does this even more often. Although some instances are "simply" teen-on-teen, almost every world ends with little Rika being disemboweled by Takano, who is an adult woman, and in one of the most gruesome arcs of the series, Shion first does a full-blown crucifixion of Satoko, then stabs her repeatedly to death.
Another straighter example, especially notable for featuring an adult woman, is when Rina attempts to strangle the barely teenaged Rena after beating her up.
Shion also brutally beats up Satoko for being too clingy to Satoshi, until Rika and Rena pull a Go Through Me to defend Satoko, and then she gets Punched Across the Room by a very pissed off Satoshi. While Satoko was extremely dependent on Satoshi, it's still no excuse for Shion almost killing much younger and weaker girl in the middle of a Yandere tantrum — and a girl who was the only good relative Satoshi still had left!
Kouga, although we only see one direct example of this. He's introduced to the story having destroyed several human villages and in the process of destroying another village - Rin's home, which is also her introduction to the storyline. On his orders, the wolves wipe out the entire village, including Rin. After that, he's more interested in fighting Naraku and winning Kagome's heart to target humans again. When his people are revisited later on in the manga, the subject of them being a human-killing race is briefly mentioned although not specifically in relation to Kouga's past.
Kagura tries to be this, but fails. She kidnaps Rin on Naraku's order but never lifts a finger against her otherwise, and when Rin's in her presence again without Sesshoumaru around, she has no interest in hurting her. She's ordered to protect Naraku's baby and, despite loathing it, she does reluctantly look after it. Hakudoushi is far crueller towards her than she ever is to him, and the detachment she appears to be closest to isKanna. In the end, she meets her death when ordered to kill Kohaku - she sacrifices herself to save his life.
In the anime, Dark MikoTsubaki is the one to blame for a then 10-year-old Kaede losing her eye. Word of God stated that Kaede actually lost her eye when Inuyasha attacked Kikyou's village in an attempt to steal the Jewel of Four Souls.
From Itsuwaribito, there is Iriya and his group of bandits, who slaughter a group of orphan children during a raid because they dislike leaving malice behind. Iriya even gloats about how they begged for their lives.
Female example: In Jackals, Roxy bisects 7 year-old Giulio Montero in one blow. Notable in that she did it directly and with her own hands. Subverted in that the child is actually an Enfant Terrible.
Several in Jojos Bizarre Adventure. Part 3 has Alessi, who straight-up refuses to fight adults because they can put up too much of a fight, and whose Stand power de-ages anybody it touches. There's also Petshop, who would have killed a young boy if it wasn't for Iggy intervening.
In the manga version of The King of Fighters spin-off KOF: Kyo, Goenitz kills Maki Kagura in front of her twin sister Chizuru when both of the twins were 10 years old. The whole thing was never shown, save for a Dead-Hand Shot of her bloodied hand.
The Anti Villains of Magical Girl Lyrical Nanoha A's, who ripped a (non-vital) organ out of a nine-year old girl's chest while she was still conscious, and later had no qualms about fighting her and her just as young friends at full power. They had a good reason to do that (at least, they couldn't see a better way to save an Ill Girl who is around the same age of the kind they attacked) and the children in question could dish it out just as well as DB heroes.
And then we have StrikerS aka the third season, where the villains strap the six-year-old Vivio to an Artifact of Doom and torture her to power it up. Some didn't seem pleased, but they didn't do a lot to stop it either.
Subaru: But this is bad, Nove! Even if both of you agreed on the fight, you shouldn't have been so harsh on a little girl.
Nove: Give me a break... I was beaten up quite badly too! It still hurts all over!
In Mobile Suit Zeta Gundam, the Titans fire their colony laser, destroying a colony in the process. Women and children are shown dying. Though not direct killing, it is a brutal sight.
The implications of their gas attacks! When we're shown the gassed colonies, we see corpses of children among the ruins.
Glemmy Toto from Mobile Suit Gundam ZZ doesn't care how many ten year old girls die fighting for him. He keeps an army of Puru clones, sending them out to do his fighting as his killing. When the clones become attached to other people, he has their successors kill them, all without the slightest hint of remorse.
This is a default in Naruto considering their world is full of Child Soldiers, the main characters included.
Nagato kills every person associated with Hanzo, including Hanzo's children and the children of Hanzo's loyalists, after Nagato wrestles control of Amegakure from Hanzo. Nagato, however, seemed indifferent to their deaths, as they were his precaution to quell any possible rebellion over his leadership in the future.
Tobi took a baby Naruto hostage, nearly spearing him with a kunai and blowing him up in the process.
Orochimaru once performed an experiment trying to infuse the DNA of the First Hokage into 60 children. One, Yamato, survived and gained his power. The rest (and to Orochimaru's knowledge until much later, all of them) died.
Captain Morgan orders a little girl be executed for seeing Zoro.
Pirate captain Zeff is a Jerkass variation. He steals and pillages and isn't above to kick little boys hard enough to send them flying, but he can also save a kid's life if he decides so.
Arlong and his treatment towards Nami, which started when she was as much 10;. In a flashback he also hits the slave girl Koala for smiling too much.
Mr. 1 and Miss Double Finger also attack a young boy when he discovers that the king was framed by Baroque Works.
There's also the Marines, who following the death of Gold Roger, searched islands he may have frequented and killed any babies born within nine months of his execution. His pregnant lover Portgas D. Rouge knew they would do this, and held Roger's child in her womb for 20 months through sheerwillpower. It ultimately cost Rouge her life, but it allowed said kid (Portgas D. Ace) to be born and raised in a more or less safe environment.
The Gorgon Sisters were sold into slavery and then tortured into insanity by the World Nobles when the eldest, Boa Hancock, was 12 years old.
Caesar Clown has no problem experimenting on little kids or getting them addicted to drugs - which would be fatal in five years - so they won't run away. His henchman Monet is no better in this regard, giving them the terrible drug with a sweet smile, fully knowing its true purpose. Even Trafalgar Law, whose infamous cruelty is legendary and has a nasty reputation among pirates, was disgusted.
Subverted in One-Punch Man when Garou is threatening to kill a child, but it's later revealed that he was just bluffing and wasn't actually going to go through with it. Played straight with several other villains though.
Accidentally occurs AND played straight in Outlaw Star due to both of the children being space pirates. The first is when Hilda, who is falling out of control towards the sun in episode 4, latches onto the Creepy Child magician girl as she is levitating towards the OLS and pulls the pin on a grenade, taking them both out. The second occurrence is when Gene and company destroy a pirate ship outside a space station that was hunting them, which was piloted by the little girl and her two cats Jim had recently befriended. He returns to the fountain to wait for them but doesn't realise why they never showed up, presuming her parents had taken her with them early.
In Pokémon Special, this is sort of a given seeing how the heroes are usually kids and the villains are adults, but it is worth mentioning that it's a rather common tactic in this 'verse to aim for thetrainer when possible.
When Hugh, who couldn't be older than eight at the time, tries to stop two Plasma grunts from running off with his sister's Purrloin, he gets a solid blow to his gut for his troubles.
In the Japanese CD dramas for Pokémon: The First Movie, after Mewtwo takes down another trainer's Magmar, Giovanni steals the Magmar, then orders Mewtwo to attack the trainer.
Several villain factions from the games are more than willing to harm Ash and his friends to accomplish their goals, including Team Galactic, TeamPlasma and Team Flare.
One of the primary antagonists in Reiko the Zombie Shop is Saki Yurikawa, a teenage serial killer responsible for the mutilation of nearly 29 little girls. There is also Reiko the protagonist's twin sister, Riruka, who actively attempts to kill a young girl summoner. Generally, most of the antagonists in this series do not believe in Infant Immortality.
And in-story, the Raid of La Bastille started when a peasant boy got shot to death in front of his parents. For worse, it was by mistake since a dumbass soldier wanted to shoot the kid's father and got the shot wrong.
In Sailor Moon S, 6-year-old Chibiusa has her heart crystal ripped out by Mistress 9. This is also played with later when Uranus and Neptune try to kill Mistress 9 as she inhabits the body of 12-year-old Hotaru, only for Usagi to defend her. This sort of works.
Also, many of the victims of the villains are children. In a memorable episode of the R season, babies were either drained of their life energy (with Manami being the only one unharmed due to Mom's intervention) or used as hostages by the monster of the week. Too bad it didn't count on Mercury getting a Mid-Season Upgradeout of pure anger.
With the exception of the Outers (Pluto since the beginning, Stars!Haruka and Stars!Michiru), the scouts are all teenage girls who fall in the 14-16 year old range.
In the first chapters of both manga/anime versions, you can see the "special" training they give to all cloth´s candidates. In the Greek Sanctuary, they push the kids/teenagers into pits with spikes and you have to climb back by yourself while avoid falling, the mess of the other bodies, and other challengers competing with you. The Kido´s foundation kids doesn´t have precisely a better treatment: they are forced to train night and day, are beaten nearly to death if they openly defy the rules (see Ikki when he confronted Tatsumi), and after some time, they are send to different places around the world for receiving heavy brutal training (things like surviving in a hot volcanic island while your sensei beat the shit out of you everyday, battling and killing grizzly bears with your bare hands, training in extreme cold conditions with not the appropriate clothing, etc), all of this only having around 10-11 years old (in fact, from the 100 kids Mitsumasa Kido sent around the globe, only ten returned...)
The Twelve Zodiac Temples Arc. Pegasus Seiya and Dragon Shiryu arrive to Cancer's Temple, and confront Cancer Gold Saint Deathkmask. The walls of said temple are covered by grim human faces, which are promptly explained to be the faces of the people Deathmask has killed in his battles. Seiya and Shiryu are both horrified and enraged when they realize that among those faces there are several children's faces. When they demand an explanation from Deathmask as to why he'd kill children, he simply states that he doesn't know how that happened, that they must have been killed along with his enemies without him realizing. Then, he calls those murders "collateral victims" and as being a nice set of ornaments for the walls of his house (remember, Cancer is the fourth temple, four is a synonym for "death" for most oriental cultures), so he basically didn't give a damn about having killed countless children, which is what immediately infuriated both Seiya and Shiryu.
In Poseidon Arc, Isaac Kraken kicks many times the poor little Kiki when he brings to Hyoga the Libra Cloth. That pisses Hyoga off enough to return to the fight.
12-year-old Chris Thorndyke from Sonic X is The Scrappy, yeah... but it still does NOT mean that he deserves to be beaten up by Shadow and later kidnapped and brutally tortured, alongside the also very young Cosmo, by Black Narcissus. The second incident is so bad that not even Dr. Eggman approves!
In Trigun, Wolfwood kills Zazie, who looks like a very young child (and is a child in the anime - in the manga, it's both complicated and frigging weird).
There's also the Gung-Ho Gun Monev the Gale, where after the shootout some of the corpses laid about were children.
Umineko: When They Cry has 9-year-old Maria Ushiromiya regularly killed off alongside the rest of the cast. While the first four times were relatively nice (explosion, explosion, strangulation, poison), the fifth time was a gaping neck wound, and the sixth was brutal decapitation. She keeps coming back to life due to a "Groundhog Day" Loop.
Maria's mother, Rosa, also physically beats her. One of their first scenes has her slapping Maria to the ground.
In Violence Jack numerous children are killed. One scene of the manga even has a girl beheaded, along with the man who used her as a human shield.
Maria from Witchblade has no problem with killing her teammates or the science institute trainees, due mostly to her own messed up childhood and not being much older herself. (They begin training at 12) She even attempts to kill Rihoko out of jealousy for receiving more of her (biological) mother's love even though they'd never met. (Her mother treated Maria completely as an experiment her whole life instead)
Shogunyan from Yo-kai Watch attempted to kill eleven-year old Nate because he wasn't respecting him.
Quite a common thing in Yu-Gi-Oh!, the most frequent victims being Yugi himself, and to a lesser extent, Jonouchi. To say nothing of Mokuba
Once he learns to trust them, Mokuba details, to Yugi and the others, how their adoptive father abused Seto.
This is even more true in Yu Gi Oh Zexal, not only because the protagonist is only twelve years old, but because every major villain in the first season seemed willing to abuse and take advantage of poor Haruto, even Dr. Faker, his own father. Although it is later revealed that Faker actually had Haruto's best interests in mind.