He portrayed Wesley Crusher on the television series Star Trek: The Next Generation, Gordie Lachance in the film Stand by Me, Joey Trotta in Toy Soldiers, and Bennett Hoenicker in Flubber.

Wheaton has also appeared in recurring voice acting roles as Aqualad in Teen Titans, Cosmic Boy in Legion of Super Heroes, and Mike Morningstar/Darkstar in the Ben 10 franchise's original continuity.

He appeared regularly as a fictionalized version of himself on the sitcom The Big Bang Theory and in the roles of Fawkes on The Guild, Colin Mason on Leverage, and Dr. Isaac Parrish on Eureka.

[10] Wheaton also appeared in Hambone and Hillie (1983), The Buddy System (1984) (opposite Richard Dreyfuss and Susan Sarandon), and The Last Starfighter.

[11] Wheaton first gained widespread attention for his work in Stand by Me (1986), the film adaptation of Stephen King's novella The Body.

[14] In her review of the film, Sheila Benson of the Los Angeles Times wrote that "Wheaton makes Gordie's 'sensitivity' tangible, but not effete.

[15] In addition to being successful at the box office,[16] Stand by Me was nominated for the Golden Globe Award for Best Motion Picture – Drama[17][18] and became known as a coming-of-age classic.

[24]Wheaton left Star Trek: The Next Generation due to concerns over how the production team addressed a scheduling conflict related to his wish to appear in the 1989 film Valmont.

[32][33] In the late 1990s and early 2000s, Wheaton appeared in several independent films, including the award-winning The Good Things (2001), in which he portrays a frustrated Kansas tollbooth worker.

[35] Wheaton regularly portrayed a fictionalized version of himself on The Big Bang Theory, becoming a recurring guest star and then side character on the show.

[41] Wheaton appeared in 12 episodes in a recurring, guest-starring role on Eureka, playing Dr. Isaac Parrish, the head of the Non-Lethal Weapons Lab at Global Dynamics and a thorn in Fargo's side.

[42] Wheaton also voices the character of the former scoutmaster and current sous-chef Earl Harlan in the popular dark, surreal-comedy podcast Welcome to Night Vale.

[44] He has hosted "2nd Watch", interviews with cast members and producers of the science-fiction series Falling Skies that appears online after each episode.

Wheaton, along with webcartoonists Jerry Holkins and Mike Krahulik of Penny Arcade, and Scott Kurtz of PvP, played in front of a live audience.

He reached the finals, defeating Troian Bellisario and Hasan Minhaj in the quarterfinals, and John Michael Higgins and Joel Kim Booster in the semifinals.

"[97] Wheaton subsequently clarified his opinion after receiving criticism, writing "I apologize to those of you who are sincere people of Faith, who felt attacked by me", but accused "the right wing noise machine" of using his comments "to deflect attention and anger away from the role that unfettered access to weapons of mass murder played in the latest incidence of mass murder in America".

[98][99][100] In September 2024, Wheaton joined other actors from the Star Trek franchise on a livestream to support the campaign of Vice President Kamala Harris in the 2024 United States presidential election.