Keenan-Bolger's regional credits include Johanna in at the Kennedy Center Sondheim Celebration in 2002, along with productions at the Goodman Theatre, TheatreWorks and Sundance Theatre Program. In 2003, she originated the role of Clara Johnson in the pre-Broadway world premiere of the Craig Lucas/Adam Guettel musical The Light in the Piazza at Seattle's Intiman Theatre and Chicago's Goodman Theatre. Her Off-Broadway credits include Kindertransport, Little Fish and Summer of '42. She appeared on the concept cast album of Bright Lights, Big City. She has sung in concert at the Lincoln CenterAmerican Songbook Series and at the Michigan Theatre with Audra McDonald. Keenan-Bolger performed as Martha in the 2005 The Secret GardenWorld AIDS Day benefit concert. In 2005, Keenan-Bolger made her Broadway debut starring in William Finn's musical The 25th Annual Putnam County Spelling Bee, where she originated the role of Olive Ostrovsky. For this performance, she was nominated for a Tony Award for Best Featured Actress in a Musical. She had appeared in the musical from its beginning at the Barrington Stage Company in July 2004, to the Off-Broadway production at the Second Stage Theatre in January through March 2005. With the original Broadway cast, she returned to The 25th Annual Putnam County Spelling Bee for a four-week limited engagement run at the Wadsworth Theatre in Los Angeles from May through June 2007. She appeared on Broadway in the revival of Les Misérables as street waif Éponine from October 2006 to April 2007, for which she received a Drama Desk Award nomination. She also participated in a reading of Shrek the Musical as Princess Fiona in 2007. Keenan-Bolger appeared in the Playwrights Horizons production of the new musical Saved with music and lyrics by Michael Friedman and a book by John Dempsey and Rinne Groff in 2008. She appeared in Bachelorette at the Second Stage Theatre and in Adam Bock's A Small Fire, opposite Michele Pawk and Reed Birney. Keenan-Bolger starred as Mary Flynn in the Encores! production of Merrily We Roll Along, which played at the New York City Center from February 8 through 19, 2012. In 2011, she starred in the New York Theatre Workshop production of Peter and the Starcatcher, a stage adaptation of the 2004 best-selling children's novel of a similar name. She reprised the role of Molly in the Broadway transfer production of Peter and the Starcatcher, which played at the Brooks Atkinson Theatre from March 28, 2012 through January 20, 2013. Keenan-Bolger received Drama Desk Award and Tony Award nominations for her performance. Keenan-Bolger played Laura Wingfield in the American Repertory Theater production of The Glass Menagerie alongside Cherry Jones, Zachary Quinto and Brian J. Smith, from February 2, 2013 through March 17, 2013. Keenan-Bolger reprised her role in the production's Broadway transfer, which ran from September 5, 2013 through February 23, 2014 at the Booth Theatre. She received a third Tony Award nomination for her performance. Keenan-Bolger starred in the Lincoln Center production of Sarah Ruhl's The Oldest Boy, which began performances at the Mitzi E. Newhouse Theater on October 9, 2014. She participated in a reading of The Brave Little Toaster: The Musical as the titular character. Others involved included Carol Channing, reprising her role as the Ceiling Fan. In early 2015, she appeared in a live reading of Eric Carle's Animals, Animals for the Autistic Children's Trust in Bangor, Maine. In 2016, Keenan-Bolger played Varya in the Roundabout Theatre Company production of The Cherry Orchard. She is currently starring on Broadway in To Kill a Mockingbird as Scout, which opened in December 2018. She received a Tony Award for Featured Actress in a Play, a Drama Desk Award, an Outer Critics Circle Award, and a Drama League Award nomination for her work.