Bakugan starts off as gender-equal in the first season, but starting from the second season, this trope is played straight, with only one girl in a team of six. Mira in New Vestroia, Fabia in Gundalian Invaders and Paige in the first half of Mechtanium Surge are the only girls in the team.
Casca is the only woman in the Band of the Hawk from Berserk and mainly serves as Griffith's Number Two. She's quite respected by pretty much the entire band, at least some of whom refer to her as "anego" (sister). In time, she becomes the Love Interest of Guts. When the Eclipse goes down, she becomes the victim of a horrific Break the Cutie ordeal, culminating in her rape at the hands of Femto right in front of Guts. Two years after the horror, she and Guts form the core of a new group of True Companions later on, which is evenly split between four guys (Guts, Serpico, Isidro and Puck) and four girls (herself, Farnese, Schierke and Evarella).
Slan is the only female out of the five God Hand members and the only truly human-looking one to boot, albeit winged naked Succubus.
In Beyblade, there are no teams with more than one girl.
The Bladebreakers add Hiromi/Hilary to their team in the second season, but not as a beyblader.
Team Psykick has multiple groups within it, but still only one female beyblader.
The pure two-man-teams, King & Queen and F-sangre/F-Dinasty, technically avert this trope, since two people isn't enough to count for the Principle.
Classi 9 is set in an all boys school and the main character, Ren, is the only girl to appear more than twice in the manga, save for the regular fangirls. It gets worse, because Ren has to crossdress to keep studying in Melite, so as far as the rest of the school is concerned the manga enters the Chromosome Casting territory.
Out of the many Shinigami to appear in the story, only Rem was revealed as explicitly female. Due to their unusual shapes, explicit declarations of male/female would be needed to determine genders, but enough others were declared male that it's easy to assume if the gender wasn't explicit, it was male, making Rem the only female Shinigami in the whole universe. Rem is also most seen with Misa Amane which is fitting.
The human cast is predominately male, due to the focus on detectives or high-ranking businesspeople, which are predominantly male groups in real-life Japan. In the Kira Task Force for the Live Action Film, where Word of God states that one female (Misa Amane) was added simply to avoid an all male team like in the anime.
Wammy's house had many gifted students, but apparently only one named female student, Linda, who appears very briefly in the manga and not at all in the anime series. note She might be in the anime Compilation MovieDeath Note Relight 2: L's Successors; the character she's supposed to be is officially unnamed. Wammy's house does have other girls in it, but none of them have any Nominal Importance or characterization, they're just extras.
Among the six Digimons that accompanies their Digidestined in Digimon Adventure 02, only one is female (Gatomon).
Digimon Frontier had an evil team of five digimon, as well as a good team of five digidestined (heroic humans) and five digimon. In each of the three groups, only one character was female.
Among the 12 Gods of Destruction, eleven are male and only Helles is female.
Android 18 is the only female member out of the ten Universe 7 fighters chosen for the Universal tournament.
Eyeshield 21 is about high school boys playing American Football. The only position a female student can have is the manager position. Unusually, as long as a team has a manager, that position is filled by a girl. Later on, the protagonist team is joined by a second girl; a prominent and active cheerleader. This moves the Devil Bats to a Two Girls to a Team example.
Riza Hawkeye is the only woman in Roy Mustang's group of Amestris Military, which consists of roughly eight men.
Amoung the four known generals of the Amestris Military, Olivier Mira Armstrong is the only female, and her staff consists of only men.
Among the... let's say seven... homunculi, Lust is the only female (though Envy is genderless according to Word of God).
In Ghost in the Shell, the only woman in Sector 9 is Major Motoko Kusanagi, and she is The Leader of seven men, not counting Tachikomas. Justified due to the fact that, while speculative fiction, it preserves the country's real world issues. Sexism in the government is dealt with explicitly in the adaption, Ghost in the Shell: Stand Alone Complex, and is a major catalyst for many of the political issues encountered later. Given this attitude, it's not unthinkable that an Elite government operations unit would have difficulty maintaining women not hyper-competent.
Jewelpet Kira Deco: Pink is the only girl in the Kira Deco 5, though there are several compensations for this; she's the protagonist, the scientist who recruted the Kira Deco 5 members is a woman, and the 5 Jewelpets who become partners to the team are all female.
In Katekyō Hitman Reborn!, there is only one female, Chrome Dokuro of the Mist, amongst Tsuna's six Guardians. Subverted, since the real Mist Guardian is Mukuro Rokudo, and Chrome is a vessel for him. Meaning instead of one woman, there's half a woman. Less than a woman. The illusion of a woman.
The anime and manga adaptations of Kin'iro no Corda: La Corda d'Oro Blue Sky has Kanade as the only female in a group of twelve guys, and is the only female in her performing group.
While there are many female characters in the main and supporting cast of Log Horizon, there is only one female member (Marielle of the Crescent Moon Alliance) out of the 11 members in the Round Table Council, the player-run government of Akihabara. This is a result of the major guilds in Akihabara mostly having male guild masters.
In the Lupin III franchise, there are five recurring characters, and Fujiko is the only recurring female character. Even she was originally only a series of several one-shot characters, as a homage to James Bond.
The director of Mai Hi ME claimed in an interview that he deliberately wanted to invert this trope. Indeed, the important male cast is considerably smaller than that of the female cast.
Sayaka Yumi is the only female (with 8 guys) at the Photon Lab Institute.
The six villains under Dr. Hell are all male. Baron Ashura is also female. Or half-male and half-female. Cyborgs.
In-universe example from Mobile Suit Gundam: Iron-Blooded Orphans: while there are plenty of female characters for the Tekkadan and Turbines, this is not the case for Gjallarhorn, Carta Issue is exceptionally the only female soldier in the entire organisation thanks to being born in House Issue, the largest family of the Seven Star, other than Carta, Gjallarhorn is run by exclusively males.
There is one female among the five Konoha Jonin senseis, Kurenai.
There is one female among the Sound Five, Tayuya.
There is only one female among the thirteen Akatsuki, Konan.
The epilogue reveals that there is currently only a single female Kage. The four male Kages are Naruto the 7th Hokage, Gaara the 5th Kazekage, Darui the 5th Raikage, and Choujuurou the 6th Mizukage. The female Kage is Kurotsuchi the 4th Tsuchikage.
The novels start with a typical fantasy adventuring group of six, which is mostly male. The sole female main character is a blond elf named Deedlit (keep in mind that this series was based on an actual Tabletop Games campaign played by a bunch of Japanese college fraternity brothers in the late Seventies — women didn't always fit well into hack'n'slash scenarios).
The sequel Chronicles of the Heroic Knight averts with a "new generation" of heroes. The party consists of three (or four) male and three female characters.
The first example of this was Ash's Bayleef in the Johto saga, the only one from that saga confirmed to be female. His Totodile is confirmed to be male, and the rest of his Johto team is heavily implied to be as well.
The Aipom Ash caught towards the end of the Battle Frontier saga was confirmed female and was the only one on his team. This trope ceased to apply to it once it was traded to Dawn.
Ash's Snivy and Unfezant from the Best Wishes saga are the only two Pokémon Ash caught in Unova that are female. His Boldore is heavily implied to be male and the rest of his Unova Pokémon are confirmed as such. Ash regularly rotates his Unova team, but almost always has Snivy in his active party, while Unfezant is usually Out of Focus and rarely needs to be called on to search for Team Rocket like his other regional birds. In fact, Unfezant was Put on a Bus for the rest of the saga once Charizard returned, making Snivy the only female member of Ash's team.
Emolga is the only Pokémon in Iris's team that is female. The other four Pokémon in her team (Axew, Excadrill, Dragonite and Gible) are all male.
Voltron (Golion) has one heroine in a squad of five heroes. Princess Allura originally only joined the team as a replacement after one member of the all-male Five-Man Band was killed. Even then, it was over everyone else's objections, and only because they couldn't form the Giant Robot without a fifth member.
Among the nine members of the Lancer team in Yu-Gi-Oh! ARC-V, only 1 member is female (Serena).
The Fourteen Lances from the backstory of Ubel Blatt had only one female member, Gustav, one of the Lances of Betrayal, although she's not the only female character in the story.