Macdonald was born in Glasgow, Scotland. Her mother was a garment industry sales executive. Her parents divorced when she was young. She and her younger brother were brought up by her mother on a council estate in the town of Newton Mearns. Macdonald attended Eastwood High School. Her family moved around frequently when she was a child.

Macdonald's career began while working as a barmaid. She saw a leaflet advertising an open casting session for Trainspotting and decided to audition, winning the part of Diane, the underage seductress to Ewan McGregor's Renton. Other roles include Mary O'Neary in Two Family House and an actress playing Peter Pan in Finding Neverland. She also had a major role in Robert Altman's British period piece Gosford Park,. where she played a lady's maid.

On television, her highest-profile roles have been in two BBC dramas, the Paul Abbott serial State of Play (2003) and the one-off Richard Curtis piece The Girl in the Café (2005). Both of these were directed by David Yates, and both also starred Bill Nighy. For her performance in The Girl in the Café, Macdonald was nominated for a Golden Globe in 2006, and won an Emmy.

After the success of previous films, such as Trainspotting and Gosford Park, Macdonald landed supporting roles in the films, Intermission (2003), as Deirdre, Nanny McPhee (2005), as the scullery maid Evangeline, A Cock and Bull Story (2006), where she plays the girlfriend of actor Steve Coogan's onscreen alter ego, Coen Brothers' Academy Award-winning No Country for Old Men, (2007), as Carla Jean Moss, the wife of the film's protagonist, where her agent originally wasn't sure she was right for the part, and Macdonald is reported as having to "fight for the role". Her persistence paid off, however, as she was nominated for a BAFTA for best supporting actress. Other films where she had supporting roles include, Choke (2008), as Dr. Paige Marshall, the film which was adapted by Clark Gregg from the 2001 Chuck Palahniuk novel, In the Electric Mist (2009), as Kelly Drummond, alongside Tommy Lee Jones and John Goodman and Skellig (2009), as Louise. She also played the lead in The Merry Gentleman (2008), as Kate Frazier. Her next project is the romantic comedy Decoy Bride opposite David Tennant.

In August 2003, Macdonald married musician Dougie Payne. The couple lives in Los Angeles. Their son, Freddie Peter Payne, was born on 9 March 2008.

BAFTA Awards

BAFTA Scotland Awards

Broadcast Film Critics Association Awards

Emmy Awards

Empire Awards