The City of Never has the death of Crystal Hopper, Alessa's younger sister who's tortured and raped for several days before finally dying after she's possessed by Draynak.
Kadu'av doesnt shy away from child murder. The Gilded Cross massacre any non-Yeshu settlements, subjecting the people to brutal deaths, and child are mentioned among the piles.
The Kindness of Devils usually avoids this trope—even None Too Holy, which puts a whole orphanage in jeopardy, doesn't kill off one child. The same can't be said for Under The Cold Moon, which goes well out of its way to show that Siegfried and Nomura have killed dozens of children.
In the M,wdyd? Series seems to be pretty consistent with killing people off in a "Kenny Death", children, especially the titular Madgie, included. The reason as to why she has it that is to usually make the story poignant and just to show anyone can die in those stories. Don't worry, they get better when time is reversed.
In Worm, the protagonistMercy Kills a toddler. The Slaughterhouse Nine also attacked a nursery at one point, albeit offscreen.
None of the stories in the Legatum series are shy about killing off children. Most notable is a case from Help Not Wanted where an ogre beats a young girl to death and then gouges out one of her eyeballs.
The story generally avoids killing actual children at least onscreen, but Tech Adventures uses this a few times. To torment Sasha some more the Joker (NOT the DC Joker) kidnaps a bus full of third graders, blowing up all the boys. He then proceeds to take to the airwaves where he tortures one girl leaving her paralyzed and dying from her injuries. Later he almost succeeds in blowing up the rest of them.
In the same story when the big bad Joanna is taking over several countries, and collecting people for mind controlled supersoldiers, her soldiers are seen killing children who are useless to her.
On Cinema: Tim's son, Tom Cruise Jr., is announced to have died near the end of season 7 and the final episode of the season is a special in his honour. Its implied that Tom's death was due to getting treatment by Dr. San rather than going to a professional doctor
Cyanide & Happiness: Too Many Police features a dad cop who uses his absurdly large family of bastard babies as meatshields, and covers the mayor in babies everywhere but the face. They both die.
Petscop: The game has a child character named Michael Hammond, who died in 1995. His name can be seen on an in-game gravestone in video 2 along with the text "Mike was a gift".