Fullmetal Alchemist: In Greedling's gang, Edward is the sole full-on human, a fact he complains about on occasion.
The Japanese exclusive Animal Crossing anime movie, in which the main character, like in the games is the only human.
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!"
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 lover), 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)
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 III has this also, given that the protagonist is a dragon in human form, other characters include Nina the wyndian (winged human), Rei the Woren (anthro tiger), Garr the Guardian (rather demonic-looking fella), and Peco the mutant (sentient onion?), this leaves us just Momo. Teepo could count, but he is only in the player's party for the first few parts of the game and is actually a dragon like the main character.
Momo has kitsune ears, so definitely not the token human.
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.
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.
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.