Walker has been twice nominated for an Academy Award and three times for a British Academy Film Award for his work on 12 Years a Slave (2013), Arrival (2016) and Blade Runner 2049 (2017). He has been nominated for the Evening Standard Theatre Award in 2009, British Independent Film Award in 2010,Satellite Award in 2011, 2013 and 2015,. He has received a string of four nominations over five years for the American Cinema Editors Award for Best Edited Feature Film - Dramatic and in 2016  he won, for Arrival. He won the European Film Award for Best Editor for Shame in 2012 and Satellite Award for Best Editing for Sicario in 2016.
Walker learned his craft in the BBC's Film Department at Ealing Studios. As a Sound Editor, he coaxed animal impersonator Percy Edwards out of retirement to provide gorilla noises for Philip Saville's series First Born. After cutting classical music documentaries for the BBC, Walker broke into editing drama with Julian Farino's Out of the Blue and comedy with two series of David Renwick's Jonathan Creek.
His first collaboration with McQueen, Hunger (2008), was a portrayal of the IRA hunger strikes at Long Kesh starring Michael Fassbender as Bobby Sands. It won the Caméra d'Or at the Cannes Film Festival. Joining again the team of McQueen, Fassbender and cinematographer Sean Bobbitt, Walker cut Shame (2011). This told the story of a successful Manhattanite navigating the terrain of sexual obsession on a path towards self-destruction. Their third collaboration was 12 Years a Slave (2013), the true story of Solomon Northup, a free man kidnapped and sold into slavery, set in 1840s Louisiana. It stars Chiwetel Ejiofor, Brad Pitt, Michael Fassbender, Lupita Nyong'o, Sarah Paulson, Paul Dano, and Paul Giamatti. 12 Years a Slave (2013) won three Academy Awards: Best Picture, Best Supporting Actress for Nyong'o, and Best Adapted Screenplay for John Ridley. In her acceptance speech, Nyong'o paid tribute to Walker, describing him as "the invisible performer in the editing room.". The film was awarded the Golden Globe Award for Best Motion Picture - Drama, and the British Academy of Film and Television Arts recognized it with the Best Film and Best Actor for Ejiofor.
Walker's partnership with Denis Villeneuve has comprised three feature films, back-to-back. Their first, Sicario, is a 2015 American crime-thriller drama film starring Benicio del Toro and Josh Brolin in which an idealistic FBI agent Emily Blunt is enlisted in a secret CIA op to bring down the head of a brutal Mexican drug cartel. Arrival is a 2016 American psychological science fiction film based on the 1998 short story "Story of Your Life" by Ted Chiang starring Amy Adams, Jeremy Renner, and Forest Whitaker. Villeneuve said of the movie's creation : "Each film has its hero. For this one, the editor Joe Walker is mine. Arrival was by far the hardest film to edit. Christ, we worked hard!". Their third collaboration is Blade Runner 2049, the sequel to Blade Runner (1982). Their fourth collaboration will be Dune (2020), based on Frank Herbert novel of the same name.
Walker has talked about time being the editor's "greatest superpower". His films with McQueen and Villeneuve showcase experiments with cross-cutting and flashback structures. McQueen has paid tribute to Walker's ability to find the rhythm of a film. "A great film editor is attuned to the silences. They can be just as valuable as the words. It's all about timing. And that's what he has - Joe has time." 
In 2010, Walker cut the documentary-feature Life in a Day for Academy Award-winning director Kevin Macdonald and producer Ridley Scott. It was filmed by YouTube users around the world on a single day in July 2010 and is distilled from the 4,500 hours of footage submitted. The movie premiered at the Sundance Film Festival in January 2011.
Walker has edited many British Indie features such as The Escapist (2008) written and directed by Rupert Wyatt; Harry Brown (2009), starring Michael Caine as a modern-day vigilante; and Brighton Rock (2010), a reworking of the Graham Greene classic that set the action against a backdrop of the Mod and Rocker riots of 1964.
Walker has cut many British TV programs: Jimmy McGovern's The Lakes; Eroica for the BBC; ITV blockbuster Doctor Zhivago starring Sam Neill and Keira Knightley; Sword of Honour for Channel 4, starring Daniel Craig; The Devil's Whore, for director Marc Munden and Tommy Tiernan for director Richard Ayoade.
Walker was initially trained as a classical composer. In 1984, he received his B.A. degree in music at the University of York. His music has been played by the Royal Philharmonic Orchestra, live in Trafalgar Square. He wrote the score for the BBC/HBO drama Dirty War. In January 2019, Joe was awarded an honorary doctorate by the University of York.