Murphy played the character of Jonathan Crane / Scarecrow in the Batman films of The Dark Knight Trilogy (2005–2012).
In the mid-late 2000s, he starred in films such as The Wind That Shakes the Barley (2006), Sunshine (2007), The Edge of Love (2008), Inception (2010) and Peacock (2010).
In 2004, he toured Ireland with the Druid Theatre Company, in The Playboy of the Western World (playing the character of Christy Mahon) under the direction of Garry Hynes—who had previously directed Murphy back in 1999 in the theatre productions of Juno and the Paycock—and also in The Country Boy. Jonathan Crane in Christopher Nolan's Batman Begins (2005).
Originally asked to audition for the role of Bruce Wayne/Batman, Murphy never saw himself as having the right physique for the superhero, but leapt at the chance to connect with director Nolan.
In 2011, Murphy won the Irish Times Theatre Award for Best Actor and the Drama Desk Award for Outstanding Solo Performance for Misterman.
He also became patron of the UNESCO Child and Family Research Centre at the National University of Ireland Galway.
He portrayed a deserting soldier who shares a grim scene with Jude Law's character, and was only on location in Romania for a week.
Murphy stated that it was a "massive production", remarking that director Anthony Minghella was the calmest director he'd ever met.
After turning down a record deal, he began his acting career in theatre, and in short and independent films in the late 1990s.
He starred as a lovelorn, hapless supermarket stocker who plots a bank heist with Colin Farrell in Intermission (2003), which became the highest-grossing Irish independent film in Irish box office history (until The Wind That Shakes the Barley broke the record in 2006).
Reflecting on his roles in 28 Days Later and the "sad-sack Dublin shelf-stacker" in Intermission, Sarah Lyall of the International Herald Tribune stated that Murphy brought "fluent ease to the roles he takes on, a graceful and wholly believable intensity.
They were offered a five-album record deal by Acid Jazz Records, but did not sign the contract; this was owing to Páidi still being in secondary school, and to the small recompense involved in ceding the rights to Murphy's compositions to the record label.
but he has said that he knew within days after starting at UCC that law was not what he wanted to do.