His first role was an unpaid appearance in a Tim Hortons summer camp commercial. That appearance eventually landed him a position in a Pillsbury commercial in which he poked the Pillsbury Doughboy, his first role with lines. He found not being cast in commercials after auditioning "really disheartening" but, in 1999, Cera was cast as Larrabe Hicks in the Canadian children's show I Was a Sixth Grade Alien, which ran for two seasons. That year, he also appeared in the television films What Katy Did and Switching Goals starring the Olsen twins. Cera then made his theatrical film debut in the science fiction film Frequency (2000) as the son of Noah Emmerich's character. Cera also appeared in the films Steal This Movie! and Ultimate G's: Zac's Flying Dream in 2000, the latter of which featured Cera in his first leading role and was presented in IMAX theaters. Cera appeared in several television films in 2001 including My Louisiana Sky and The Familiar Stranger and also began voicing Josh Spitz in the animated series Braceface, continuing to do so until 2004. In 2002, Cera played the young Chuck Barris (played by Sam Rockwell) in the George Clooney-directed film Confessions of a Dangerous Mind. He provided the voice for Brother Bear – an anthropomorphic bear – in the 2003 The Berenstain Bears animated series, which aired for three seasons.

Following a role in the critically panned unaired Fox pilot The Grubbs in 2002, Cera successfully auditioned for a part in another Fox sitcom, Arrested Development, which began airing in November 2003. The show follows the formerly wealthy and dysfunctional Bluth family, with Cera playing George Michael Bluth, the teenage of son of Jason Bateman's character, Michael Bluth. After three seasons, Fox canceled the series in 2006 due to low viewership despite critical acclaim. In 2006, he created and starred in a parody of Impossible is Nothing, a video résumé created by Aleksey Vayner. Cera and his Arrested Development co-star Alia Shawkat guest starred as a pair of college students in the teen noir drama Veronica Mars in the episode "The Rapes of Graff" in 2006. Along with best friend Clark Duke, Cera wrote and starred in a series of short videos released on their website. The idea came from Duke, who was enrolled at Loyola Marymount University and did it for his film school studies. In 2007, they signed a deal with CBS Television to write, produce, direct, and act in a short-form comedy series entitled Clark and Michael. The show featured guest stars such as David Cross, Andy Richter and Patton Oswalt, and was distributed via CBS's internet channel, CBS Innertube.

In November 2007, Cera hosted an untelevised live staged version of Saturday Night Live, not broadcast due to the then-ongoing 2007 Writers Guild of America Strike. In his second film of 2007, Cera co-starred in Juno as Paulie Bleeker, a teenager who impregnates his long-time school friend Juno (played by Ellen Page). For Superbad and Juno, Cera won Breakthrough Artist in the Austin Film Critics Association Awards 2007 and was included in Entertainment Weekly's 30 Under 30 list in February 2008. Cera starred alongside Kat Dennings in the romantic comedy-drama Nick & Norah's Infinite Playlist (2008), in which they played two strangers who bond over their shared love of a band and try to find their secret show. He then starred in the comedy Extreme Movie (2008), which was composed of vignettes focusing on teen sex. Cera held a recurring role on the comedy series Childrens Hospital from 2008 to 2016 as Sal Viscuso, a hospital staffer who is only ever heard through an intercom.

Cera played a fictionalized version of himself in the independent romantic comedy Paper Heart (2009), which followed the fictional relationship between Cera and the film's Writer Charlyne Yi, also playing herself. Cera and Yi composed the film's score together. Cera then starred opposite Jack Black in the comedy Year One, set during the Stone Age. The film, directed Harold Ramis, was poorly received, although Time magazine critic Mary Pols felt Cera's performance saved the film from being a "catastrophe". In his final film of 2009, Cera starred in Youth in Revolt, an adaptation of the eponymous novel. He played a shy teenager named Nick Twisp who creates a destructive alter ego, François Dillinger, after becoming smitten with a girl, who is played Portia Doubleday. Cera's first published short story, "Pinecone", appeared in McSweeney's Quarterly thirtieth issue. Cera was cast as Scott Pilgrim in the film adaptation of the graphic novel series by Bryan Lee O'Malley after the film's Director Edgar Wright had seen Arrested Development and needed an actor "audiences will still follow even when the character is being a bit of an ass". The film, Scott Pilgrim vs. the World, follows Pilgrim, a musician who must battle the seven evil exes of his girlfriend Ramona (played by Mary Elizabeth Winstead). It was released in cinemas in August 2010, whereupon it became a box office bomb after just grossing $47.7 million against a production budget of $85–90 million.

Cera made a guest appearance in "The Daughter Also Rises", a 2012 episode of the animated sitcom The Simpsons as the voice of Nick, a love interest to Lisa Simpson. Cera made his theater debut in a production of Kenneth Lonergan's play This Is Our Youth in a two-week run during March 2012 at the Sydney Opera House. The play also featured his Scott Pilgrim co-star Kieran Culkin and Tavi Gevinson. A Broadway production at the Cort Theater opened in September 2014 and closed in January 2015. The New York Times theater critic Ben Brantley praised Cera for achieving "something remarkable": "the sense of an amorphous being assuming and losing shape in the course of roughly 12 hours". Also in 2012, Cera played a supporting role in the drama The End of Love and appeared in the short film The Immigrant. Arrested Development was revived for a fourth season in 2012 by Netflix, with Cera reprising his role as George Michael. Cera worked in the writer's room and served as a consulting Producer during its production. The season was released in May 2013.

Cera collaborated with Chilean filmmaker Sebastián Silva on two films in 2013 – Magic Magic and Crystal Fairy & the Magical Cactus – both of which were filmed in Chile and premiered at the 2013 Sundance Film Festival. He spent "five hours a day learning Spanish" for Magic Magic. Cera was featured most prominently in Crystal Fairy, in which he starred as a self-absorbed man travelling Chile with a woman named "Crystal Fairy" (played by Gaby Hoffmann) while bearing a cactus. Along with Reggie Watts, Tim & Eric, and Sarah Silverman, Cera created the web-based comedy YouTube channel Jash in March 2013, where he has postsed short films which he directs and/or stars in. These films include the comedy-drama Gregory Go Boom (2013), in which Cera played a paraplegic man, and his directorial debut Brazzaville Teen-Ager (2013), co-starring Charles Grodin as his sick father. He played an exaggerated version of himself in the apocalyptic comedy film This Is the End, which was released in summer of 2013 and featured his Superbad co-stars Jonah Hill and Seth Rogen. Throughout 2013, Cera also appeared on Burning Love, a web spoof of reality dating competition shows, and on an episode of Drunk History as John Endecott. Cera had previously played Alexander Hamilton in a comedic retelling of Hamilton's duel with Aaron Burr on the show's first episode as a web series in 2008 before it was adapted into a television show.

In 2010 Cera contributed mandolin and backing vocals to the Weezer song "Hang On" from their album Hurley. Cera has also established himself as the touring bass player in Mister Heavenly, an indie rock band originating in the American North West, and is a member of the band The Long Goodbye, along with Clark Duke. Cera also played bass and sang back up during songs in both Scott Pilgrim vs. the World and Nick and Norah's Infinite Playlist. He released his full-length debut album True That on August 8, 2014 through his official Bandcamp page. The album features 19 original tracks, a cover of Roderick Falconer's "Play It Again" as well as a cover of Blaze Foley's "Clay Pigeons."

In early 2015, Canadian musician Alden Penner released "Meditate", a track from his upcoming EP Canada in Space, which features Cera. Penner subsequently announced that the EP would be released on 29 June 2015 on City Slang records, as well as a European tour of the UK, Netherlands, France, and Germany, which featured Cera as both co-headliner and member of Penner's backing band. The song "Best I Can" from the film Dina, written and performed by Cera and featuring Sharon Van Etten, was unsuccessfully nominated for Best Song In A Documentary at the 2017 Critics’ Choice Documentary Awards.

A "giant fan" of Director David Lynch, Cera made a guest appearance in the 2017 revival of Lynch and Mark Frost's television show Twin Peaks in the show's fourth episode, as Wally "Brando" Brennan, the son of Deputy Sheriff Andy Brennan and Lucy Brennan. The appearance contained several references to the work of actor Marlon Brando as Wally shares the same birthday and is nicknamed after Brando. Cera returned to the stage in March 2018, starring in a second Kenneth Lonergan production, Lobby Hero, at the Helen Hayes Theatre on Broadway. The play also stars Chris Evans, Brian Tyree Henry and Bel Powley. In 2018, Cera will co-star in the upcoming drama Gloria, starring Julianne Moore as the title character, and will star in the animated comedy Blazing Samurai as a dog who wishes to become a samurai. Cera will also return to his role as George Michael in the fifth season of Arrested Development in 2018.