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. Her mother is a piano teacher and taught her when she was a young child, and her father worked in the printing trade. 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. After Cambridge, she pursued postgraduate studies at the Royal Academy of Music. She became Head of Piano at the Royal Academy of Music in 2011.