MacGregor grew up in North London, and was educated at home, with her brother and sister, by her parents; she won a free place to South Hampstead High School at the age of 11.

MacGregor began studying with Christopher Elton at the age of seventeen, and read music at New Hall (now Murray Edwards College, Cambridge) (1978–81) where she was taught composition by Hugh Wood.

In the early years of her performing career, MacGregor was a prolific composer for the theatre (including work for Cheek by Jowl, and Oxford Stage Company's production of Hamlet at Elsinore Castle and the Edinburgh Festival).

The conductors with whom she has worked include Pierre Boulez, Sir Simon Rattle, Sir Colin Davis, Michael Tilson Thomas, and Valery Gergiev, and she has appeared in many of the world's greatest venues, including the Wigmore Hall, Southbank Centre and the Barbican in London, Sydney Opera House, New York's Lincoln Center, Leipzig Gewandhaus, the Concertgebouw in Amsterdam and the Mozarteum in Salzburg.

MacGregor is particularly known for her Bach interpretations and recordings, and was invited by Sir John Eliot Gardiner to perform the Goldberg Variations at the Royal Albert Hall in April 2013.

MacGregor made her conducting debut in 2002 and regularly directs her own orchestral projects, including an all-Mozart programme with the Royal Philharmonic Orchestra and Bach with the Hallé.

She enjoys a close artistic partnership as conductor and performer with Britten Sinfonia, in programmes ranging from classical music to collaborations with jazz and world musicians, including Andy Sheppard, Seb Rochford, Nitin Sawhney and Arve Henriksen.

In 2009 she opened the London Jazz Festival with Britten Sinfonia and Arabic singer and oud virtuoso Dhafer Youssef, hailed by The Times as 'the future of music'.

The books feature storytelling, cartoons, games and include companion CDs, with music ranging from classical and jazz to gospel and hip hop.

MacGregor was appointed as Member of the Arts Council England in 1998 alongside Anish Kapoor, Brian McMaster, Anthony Gormley and Andrew Motion, leaving in 2004.