Fox was born in Hammersmith, London, England. She comes from a thespian family — her mother is actress Joanna David (née Joanna Elizabeth Hacking) and her father is actor Edward Fox. Her uncle is James Fox and her cousins Jack, Laurence and Lydia also have successful acting careers. She has a brother Freddie, also an actor, and a half sister Lucy. She was educated at the independent Bryanston School where she played the cello, and at St Catherine's College, Oxford, where she read English. Her great-great grandfather was Samson Fox, a self-made millionaire, and her great-grandmother was the actress Hilda Hanbury, sister of Lily Hanbury. Her grandfather was Robin Fox, a theatrical agent. Through Hanbury, she is related to the Terry family of actors.
In 2000 Fox was engaged to the comedian Vic Reeves. In July 2005, she married the British actor Jared Harris, the son of the Irish actor Richard Harris. The couple announced their split in 2008, and Harris filed for divorce in January 2009. The divorce followed the breakdown of their long-distance relationship and her having a miscarriage in 2007.
Fox later entered into a relationship with actor Jeremy Gilley, and in May 2010 it was reported that Fox was pregnant with their child. The Harris-Fox divorce was finalised in June 2010. In November 2010, Fox gave birth to a baby girl named Rose.
Fox is a patron of the environmental and human rights charity the Environmental Justice Foundation. She speaks German and French. She plays the cello, the piano and the trumpet.
Fox first appeared as Georgiana, the sister of Colin Firth's Mr. Darcy, in the 1995 television adaptation of Pride and Prejudice, followed by her role as the second Mrs. de Winter in the 1997 television adaptation of Rebecca opposite Charles Dance. In 1998 she starred with Ben Miles in the adaptation of Catherine Cookson's The Round Tower as the young Vanessa Radcliffe, a wealthy girl from an affluent family who is forced to leave her home after becoming pregnant. Fox played Jeannie Hurst in the 2000 remake of Randall and Hopkirk. In 2003, she played Jane Seymour in a two-part television biographical film about King Henry VIII. She also played the title role in Katherine Howard, directed by Robin Lefevre at the Chichester Festival Theatre in 1998.
In 2004, she joined the cast of the crime drama, Silent Witness & as of 2017, she is still in the show and has now played the role of Nikki Alexander for 13 years. Also, in 2004, she played Lady Margaret in Part 2 of Gunpowder, Treason and Plot, the mini-series about James I (James VI in Scotland) and the Gunpowder Plot. In 2005 she played Rosie Jones in the film Keeping Mum and in 2008 she played Sister Jean in Baillie Walsh's Flashbacks of a Fool with Daniel Craig. She also starred in Things To Do Before You're 30, with Billie Piper, who would later marry her first cousin Laurence Fox. She was cast as Lynne Frederick in the 2004 film The Life and Death of Peter Sellers starring Geoffrey Rush in the lead role. A whole section of the film focusing on the Frederick/Sellers relationship was removed in the final edit. (She can be seen briefly in a background shot towards the end of the film) The deleted scenes with Fox can be found with others among the special features on the DVD release of the film.
2007 saw Fox reunited with her Rebecca co-star Charles Dance when they starred together in the ITV1 mini-series Fallen Angel, which saw Fox as serial killer Rosie Byfield, with Dance appearing as her father. The rewind format in which the show was shot traced the development of the killer streak of Fox's character. (Fox and Dance both appeared in ITV1's Henry VIII, but Dance's role of the Duke of Buckingham was limited as his character was arrested for treason less than fifteen minutes into the first half, while Fox's scenes as the doomed third Queen Jane Seymour dominated the first half of the second episode). In the 2008 English language DVD re-release of the cult 2006 Norwegian animated film Free Jimmy, Fox voiced the character of "Bettina". The dialogue was written by Simon Pegg and other actors included Pegg himself and Woody Harrelson. Emilia Fox narrates the popular children's book We're Going on a Bear Hunt (by Michael Rosen and Helen Oxenbury) with Kevin Whately in a special edition book and DVD set. She appeared as Morgause in the second series of BBC's Merlin in 2009. She returned for the third series and the fourth. Also in 2009, she portrayed Queen Elizabeth II in the Channel 4 documentary entitled The Queen.
For Doctor Who she narrated the character, Lady Winters, in the Doctor Who Adventure Game, The Gunpowder Plot, (2011). She previously played Berenice in the Eighth Doctor audio drama Nevermore.