She has written a string of plays which are set in the fictional town of Shirley: Body Awareness (2008), Circle Mirror Transformation (2009), The Aliens (2010), and Nocturama (2014).

[6] Circle Mirror Transformation premiered Off-Broadway at Playwrights Horizons[7][8] in October 2009 and received the Obie Award[9] for Best New American Play and Performance.

[10][11][12] The Aliens, which premiered Off-Broadway at Rattlestick Playwrights Theater in April 2010, was a finalist for the 2010 Susan Smith Blackburn Prize and shared the 2010 Obie Award for Best New American Play with Circle Mirror Transformation.

[9][13] Her adaptation of Anton Chekhov's Uncle Vanya premiered at the Soho Repertory Theatre in June 2012, running through August 26, and was called a "funky, fresh new production" by The New York Times reviewer.

[14] Directed by Sam Gold, the cast featured Reed Birney (as Vanya), Maria Dizzia, Georgia Engel, Peter Friedman, Michael Shannon (as Astrov), Rebecca Schull and Merritt Wever (as Sonya).

[26] John won the 2016 Obie Awards for Performance for Georgia Engel and a Special Citations: Collaboration, for Annie Baker, Sam Gold and the design team.

[33] In September 2023, Baker's "weird and great new play," Infinite Life, opened at Off-Broadway's Atlantic Theater Company directed by James Macdonald and featuring Christina Kirk, Mia Katigbak, Kristine Nielsen, Brenda Pressley, Marylouise Burke, and Pete Simpson.

[36] Tomris Laffly of TheWrap wrote in a mixed review that "[the film] keeps the viewer at arm’s length from both the joys and aches of tweenhood, when all you crave is to get just a step closer.

[43][44] In July 2017, Baker was among 60 artists who signed an open letter organized by the group Adalah-NY that called on Lincoln Center to cancel performances of a play sponsored by the Israeli government and based on a novel by David Grossman.

[47] Time Out New York wrote in 2008 that Baker "creates normal individuals coping with everyday issues in their small-town lives," and that her play Body Awareness "marks the arrival of a new playwright who would seem to fit the quirky bill, but aims for sincerity instead.

"[48] The New Yorker said Baker "wants life onstage to be so vivid, natural, and emotionally precise that it bleeds into the audience’s visceral experience of time and space.

Drawing on the immediacy of overheard conversation, she has pioneered a style of theatre made to seem as untheatrical as possible, while using the tools of the stage to focus audience attention...."[1] The website The Daily Beast found that, "Baker’s skill is to make us work hard as an audience to make our own sense of her play[s] — the best, most enriching way to view any theatrical performance.

[56] A new play, titled The Last of the Little Hours, written by Baker was chosen for development at the Sundance Institute's 2014 Theatre Lab in Utah to be presented in July.