Runcie is the son of Robert Runcie, the former Bishop of St Albans and Archbishop of Canterbury, and Rosalind Runcie. He was educated at the Dragon School in Oxford, Marlborough College, and Trinity Hall, Cambridge. He gained a First Class degree in English from Cambridge University in 1981.

Runcie married the Radio Drama producer Marilyn Elsie Imrie in 1985. They have one daughter together, Charlotte Runcie, born in 1989, and James is also stepfather to Marilyn's daughter, Rosie Kellagher, born in 1978. Kellagher is a freelance theatre director. Charlotte is currently studying at Queens' College, Cambridge University.

The family currently lives in Edinburgh, Scotland.

From 1983-1985, Runcie worked in Radio Drama for BBC Scotland as a writer and director. His work included Miss Julie, The White Devil, Roderick Hudson, Men Should Weep, and A Private Grief.

More recently, James Runcie has produced Arts, Music, and History programmes for the BBC. He is a freelance director of documentary films, and has produced documentaries such as J.K. Rowling: A Year in the Life for ITV, My Father (on his father Robert Runcie), and a six-part series How Buildings Learn. He works freelance for the BBC, ITV, and Channel 4. He has worked with presenters including David Starkey, Griff Rhys Jones, Andrew Motion, Alain de Botton, and Simon Schama.

James Runcie filmed the documentary My Father a week before Robert Runcie's death. It contains the last interview with the former Archbishop.

In 2009, Runcie was appointed Artistic Director of the Bath Literature Festival.

From October 2006 to October 2007, Runcie spent a year filming J K Rowling as she worked on completing the final novel in the Harry Potter series, Harry Potter and the Deathly Hallows. The programme featured intimate access to Rowling's daily life, and included deeply personal interviews about her childhood and her own struggles with her writing process. The film frequently shows Rowling in tears when she remembers her life before writing Harry Potter. It is particularly notable for documenting the moment Rowling finished writing the final book. The film received positive reactions amongst the online Harry Potter fan community. Runcie conducted his own interviews and narrated the film, however, when shown in the United States, additional commentary was provided by Elizabeth Vargas.

Runcie has written four novels: Canvey Island, The Discovery of Chocolate, The Colour of Heaven, and East Fortune. He is published by Bloomsbury.

He also frequently writes lifestyle pieces on the subjects of family and literature for major UK newspapers.

Runcie won a Royal Television Society award for his film Miss Pym's Day Out in 1992, and has also received Royal Television Society nominations for How Buildings Learn and The Gentle Art of Making Enemies. Miss Pym's Day Out was also nominated for a BAFTA Huw Wheldon Award for the Best Arts Programme in 1992.

He has won two BAFTA Scotland Radio Drama Awards for Watching Waiters and Mrs Lynch’s Maggot, and been nominated for a BAFTA award for the film Great Composers — Bach.