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If you count Human Aliens as non-humans, Nanoha and Hayate would be the only humans from Earth. Funny enough, they are the foreigners since the setting is mostly on Mid-Childa or elsewhere outside from Earth.
The trope is inverted if you look the Special Duty Section Six as a whole. They are actually more human members than non-humans.
The Hückebein Family seem to have Sonica Lilian as the only non-Eclipse Driver.
Hayate is the only real human of the Yagami family. The others are four living programs and two Unison Devices.
The Big Bad of Usagi Yojimbo, Lord Hikiji, is the only human in the setting. He's only been shown unmasked once, right at the start of the series, and creator Stan Sakai has since said he regrets making him human. (Since that time, barring a couple of brief flashbacks where he turns up so heavily armored that his species cannot be discerned, the character has only been alluded to.)
Rankorr of the Red Lanterns series is very much a Token Human — the comic even openly declares "The first HUMAN Red Lantern!"
A Voice Among The Strangers token human is Jessica, a Filipino mix that got sucked into Equestria by a book. She also doesn't understand the language at first.
Bait and Switch (STO): The USS Bajor's command staff contains only one human, the chief medical officer Warragul Wirrpanda, and he's not even from Earth. The rest of the command crew are two Bajorans (captain and ops officer), two Andorians (first officer and chief engineer), a Trill (science officer), and a Pe'khdar (security chief).
Justified with Lieutenant Commander Jaleh Khoroushi from "Aen'rhien Vailiuri". She's a human Starfleet officer serving aboard a Romulan Republic ship as a liaison officer, and is explicitly the only human on the entire ship.
Tully in the the Chanur Novels. Not only is he a Token Human, but he's a non-viewpoint secondary character with hardly any dialogue. In spite of all that, though, his presence is the catalyst which drives the story.
Bren Cammeron from the Foreigner series. Being a diplomat who's the only human allowed off the human enclave of Mospheira, he spends most of his time in the company of the alien atevi.
Alan Dean Foster's Spellsinger novels have only two ( three, if you count the Son of Spellsinger) major human characters, including The Hero Jon Tom. All others are anthropomorphic animals.
Stephanie from LazyTown. She's the only human child, and the only female human, even though her uncle and every other townsperson is a puppet. The other two humans are the hero and the villain. Extra points for being the new kid, totally unfamiliar with the puppets' weird ways.
Every now and then, Doctor Who has a situation like this.
At one point, the Team TARDIS was three Human Aliens and Tegan, a human from Australia.
There's also the Paternoster Gang, a crime-fighting team in Victorian London that comprises of Madame Vastra (a Silurian), Jenny (her human maid and wife), and Strax (a Sontaran), with the Doctor occasionally joining them as well.
Mike/Joel on Mystery Science Theater 3000, not counting the various crazy people sending him movies. They both spend most of their time surrounded by highly neuroticrobot "friends", occasionally leading to jokes (typically in the host segments) about the 'bots not understanding a human custom or vice-versa.
The Muppet Show usually had one human guest and all muppets otherwise, though some muppets are human-like muppets.
Every so often, the cast of Being Human picks up one. They tend to not last, though. The most prominent would be Nina (until she is turned into a werewolf) and Lucy (until she was murdered)
Teen Wolf: Stiles is this as of season 4 (not counting the adults), after the death of Allison and the reveal that Lydia is a Banshee.
For a while, Mr. Reed was the only "human" member of Steam Powered Giraffe, until the addition of drummer Sam Luke and sound engineer Steve Negrete.
Following the recent departure of Mr. Reed and drummer Matt Smith, Steve Negrete now fills this role. (The jury's still out on the Walter Girls.)
Can happen in about any fantasy/sci-fi roleplaying game where humans are only one of the playable races.
The Yu-Gi-Oh! TCG have Bladefender and Flowerknight, two of the monsters among the ranks of the Sylvans. The Sylvans are nature spirits taking the form of plantlife (or in the case of their strongest monsters, plant/animal hybrids). Bladefender and Flowerknight are exceptions to this, being completely human in appearance, instead wearing clothing and weaponry made of flowers and leaves. Despite this they are still classified as plants, meaning they're not actually human, despite looking the part.
While all the characters mostly look human in appearance, Claude is the only actual human on the team in Star Ocean 2.
The player in Pokemon Mystery Dungeon. While not exactly a human at the moment, you were in the future, before you transformed, and are the only human even mentioned.
Averted in In Gates to Infinity; other humans turned Pokémon were mentioned but were never interacted with and were only seen as balls of light returning home, having failed the same mission you were summoned for.
Breath of Fire IV averts this, as there are no humans in the player's party. The protagonist looks like a human but is actually the second half of an ancient dragon god and the others being a wyndian, woren, sentient armor, anthropomorphic dog and a humanoid with kitsune-like features.
The player character in Hatoful Boyfriend, the only human at a school for... sapient birds.
Yuuya (paraphrased): You stand out like a poppy in a field of rye.
Dr. Cain in Mega Man X series is one of the very few "living" humans shown in-game.
For a franchise where robots and their effect on human society is a major theme, many of the series in the Mega Man franchise are pretty sparse on humans. Mega Man classic only has Dr. Light and Dr. Wily, with Dr. Cossack and Kalinka only playing a major role in a single game, and Mega Man Zero has Ciel and series Big Bad Dr. Weil, though he's barely human by the time he's introduced, though Zero 4 eventually introduces an entire convoy full of humans to the cast.
The massively underratedAarklash Legacy from Cyanide Studios, features a Ragtag Bunch of Misfits, and nearly all of them are monsters and fantastical creatures. The party includes, but is not limited to, a velociraptor/kangaroo cyborg mutant lady, a rat-worshipping goblin Gentleman Thief, a psychotic cannon-wielding dwarf, a Caribbean Orc wise-man healer, and a Lich. The only exception is the leader of the party, Nella, a human Hot Witch.
Possibly the case in Final Fantasy IX. Zidane is a genoms, Vivi is a Black Mage, an artificial life form, Garnet is a Summoner, Freya is a Burmecian, Quina is a Qu, and Eiko is a Summoner. Amarant is never said to be non-human, but he has blue skin and rather strange hair, and there are plenty of unnamed but clearly non-human races around in world in the form of NPCs. It's possible that Steiner is the only outright human in the group.
Vegeta in Ducktalez, as he's the only Human Alien in a Newgrounds cartoon where everyone else in the main cast is a duck.
Furthia High: Not only the sole human in the cast but possibly the sole human in the world.
Tip, token human of Skin Horse, is just as eccentric as his friends, being a Wholesome Crossdresser. Though the rest of the team consists of a transgenic superdog, a crazy zombie, a clockwork killer robot, a swarm of bees, and a helicopter with a human brain in a jar.
At first glance, Francis Fennec in Kevin & Kell looks like this, the only human in a world of Funny Animals. The truth is a lot more complicated. In the first place, Francis was born a Funny Animal as well, albeit of indeterminate species, and spontaneously turned human later. And the other thing is, Domain is the parallel dimension of the human world. Francis's mother Danielle originated from there and turned into a Funny Animal when she crossed the portal into Domain. It's strongly implied that, despite genetically being a rabbit, Danielle's origins as a human enabled Francis to become a human. The implications are not lost on Lindesfarne, another former human.
Beast Wars and Beast Machines are the only Transformer series' not to have human companions (there are proto humans in Wars, but they rarely show up).
Elisa from Gargoyles for a time until other human characters become engraved in the story.
Robin is the only vanilla human member of the Teen Titans. Cyborg and Beast Boy started as humans, but nowadays the former is, well, a cyborg and the latter is a green-skinned shapeshifting mutant. Raven is half-human, half demon lord, and Starfire is a flat-out alien.
The forest ranger and his family in The Raccoons, who were the original owners of Bruu, though not long after the humans were phased out entirely. Though since they never actually interacted with the anthropomorphic animals they may not count for this trope.
Although not the token human among the main set of characters, Margaret's father among her family in Regular Show.
Uncle Grandpa is the only human on the RV, though most of the kids he helps are also humans.