Supporting
Frank the Pug (voiced by Eddie Barth) – Frank the Pug is an extraterrestrial living in New York City, in the guise of a pug. It is later revealed that the "human" at Frank's newspaper stand is a robot, and that Frank's true form resembles a pug, albeit with a dark green color, antennas, and a three-pointed tail.
The Worm Guys (voiced by Patrick Pinney and Pat Fraley) – The Worm Guys are four insect-like aliens who love to drink coffee and relax in the organization's break room, all of their names are Neeble, Geeble, Sleeble and Mannix. They are renowned for knowing many figures of speech and the organization rulebook.
Jack Jeebs (voiced by Tony Shalhoub in Season 1, Billy West in Seasons 2–4) – Jack Jeebs is a humanoid alien who runs a pawn shop, carrying both alien and human merchandise. Jeebs' head is frequently blasted off, but he possesses regenerative abilities that let him grow his head back within seconds, much to his annoyance.
Idikiukup and Bob (voiced by Patrick Pinney and Pat Fraley) – A pair of alien twins (earning them the nickname of the Twins) that serve as the MIB's head scientists along with Agent L. They mostly stay at headquarters, though Bob pilots a helicopter in "It's a Fmall Fmall World".
Dr. Zan'dozz Zeeltor (voiced by Steve Kehela) – A blue-skinned humanoid alien who replaces Elle as chief scientific officer of the organization. He is very eccentric about the simple items around Earth. Most of his inventions usually cause more harm around J, such as a sticky note pad that started to constrict him. Zeeltor has a pet named Lucy: a Futavian bacteria colony.
Agent X (voiced by Adam Baldwin) – A big-eared, green-skinned alien from the G-Dan galaxy; recruited into the organization as Elle's partner, to smooth over human-alien relations. Though he has an impeccable record, X was suspended six times in his home galaxy.
Agent D (voiced by John Mariano) – Agent D (Derrick Cunningham) is Agent K's former partner who is now retired after getting too old in the fight against the evil aliens. He was a founding member of the organization. Derrick is seen enjoying his retirement with his wife, before he is wiped out of existence by a time traveling alien-hating bigot. Agent D was restored by K and a Cerebro-enhanced Agent J.
Agent H (voiced by Kurtwood Smith) – One of the founding members of the Men in Black. He was responsible for designing most of the organization's medical equipment.
Agent Q – One of the founding members of the organization; responsible for the weapons and vehicles that the organization use.
Aileen (voiced by Beth Broderick) – A female alien and agent of the Men in Black: a blue-skinned humanoid with extendable, tentacle-like fingers. She lost her former partner to an alien shapeshifter called an Inanimate. She is later assigned another partner named Eidi, whom she treats similarly to K's treatment of J. Like K, she is a legendary agent on her home planet.
Eidi – Aileen's rookie partner who belongs to the same species as her and was assigned to work with her after the capture of the Inanimate. Eidi and J bond while working the case due to their shared status as novices partnered with the planet's best agents.
Agent U – An average agent. His name before joining the organization was Upton, which J easily deduces. There is a running gag where U's agent codename and the word "you" are often confused. U is shown to be a major suck up and simply teaches alien children how to disguise themselves as humans.
Agent E – An agent who works in Hollywood, getting work for aliens in movies and television shows.
Troy The Symbiote (voiced by Rino Romano) – A young adventurous symbiote who has a playful relationship with J. His dream is to work for the organization, much to his mother's distress. Troy becomes an MIB intern in "The Heads You Lose Syndrome".
Klah'Mikk – A paperwork-filing alien who works for the organisation.
The Fmeks – The warmongering counterparts of the Arquillians. The Fmeks are the Arquillians' sworn enemy because the Arquillians' planet is bigger than their home world Fmoo.
