Butterworth has had major success with his play Mojo (which premiered at the Royal Court Theatre in 1995). It won the 1996 Laurence Olivier, an Evening Standard , The Writer's Guild and the George Devine awards, and the Critic's Circle Award. Butterworth wrote and directed the film adaptation of Mojo, released in 1997. The film featured Harold Pinter. A major influence on Butterworth's work is 2005 Nobel Literature Laureate Harold Pinter: "I know and admire Harold Pinter enormously. He has a ginormous influence on me. Conversations with him have inspired my work."

He directed and co-wrote with his brother Tom the film Birthday Girl (2001), which was produced by his brother Steve and starred Nicole Kidman.

Butterworth received positive reviews of his play The Night Heron, which premiered in the West End at the Royal Court Theatre in 2002. The Guardian reviewer wrote: "Can a play be simultaneously very good and very bad? I believe so." The Winterling also ran at the Royal Court in 2006. The britishtheatreguide wrote: " 'The Winterling' can be a difficult play but contains rich veins of comedy."

In May 2007 Butterworth received the E. M. Forster Award from the American Academy of Arts and Letters.

His play Parlour Song opened to "rave reviews" at the Atlantic Theatre Company, Off-Broadway in March 2008. The Almeida Theatre presented its European première in March 2009.

Butterworth's fourth play for the Royal Court Theatre was the comedy Jerusalem, which premiered in July 2009 to positive reviews. Described as a "contemporary vision of life in [England's] green and pleasant land", Jerusalem was the second important Butterworth production in London in 2009. The production starred Mark Rylance as Johnny Byron, and featured Mackenzie Crook as Ginger in a supporting role. It was a sell-out at the Royal Court, won the Evening Standard Theatre Award and Critics' Circle Theatre Award for the best play of 2009 and, with the same cast, transferred to the Apollo Theatre on Shaftesbury Avenue in January 2010. Jerusalem opened on Broadway in April 2011, with many of the original UK cast. It returned to London later that year, again playing at the Apollo. In January 2014 Jerusalem opened at the San Francisco Playhouse, where it also received rave reviews. Jerusalem was nominated for the 2011 Tony Award, Play and Mark Rylance won the 2011 Tony Award for Best Performance by an Actor in a Play.

Jez and John-Henry Butterworth were named recipients of the Writers Guild of America West's 2011 Paul Selvin Award for their screenplay for the film Fair Game (2010), directed by Doug Liman and starring Naomi Watts and Sean Penn.

On 26 October 2012, Butterworth's play The River opened at the Royal Court Theatre, starring Dominic West, Laura Donnelly and Miranda Raison, with an appearance by Gillian Saker. The River had its US premiere on Broadway at the Circle in the Square Theatre in a limited engagement in October 2014, starring Hugh Jackman and directed by Ian Rickson. Reception was positive, with London critics finding the work "lyrical"; "beautifully written" and "suffuse[d] with wonder and beauty".

Butterworth's most recent play, The Ferryman, opened at the Royal Court Theatre in April 2017. Directed by Sam Mendes, it became the fastest selling play in the Royal Court Theatre's history. Set in Rural Derry in 1981 and focussing on the events surrounding the deaths of the IRA hunger strikers, it received 15 five-star reviews, including all the major UK papers. The Irish Times said "Although Butterworth is English, The Ferryman feels like a thoroughly Irish play, not only because there is not a single false note in the dialogue." The Huffington Post called it "one of the two or three greatest plays of the decade". However, The Guardian 's Sean O'Hagan wrote "I'm from Northern Ireland and it doesn't ring true". Two weeks later The Irish Times printed an article entitled "In defence of The Ferryman" which directly challenged Sean O'Hagan's claims, calling the play "layered and powerful".