Harris was born and raised in London, England, the daughter of sitcom writer Lisselle Kayla, a single mother who had emigrated to England from Jamaica as a child. After graduating in 1998 from Pembroke College, Cambridge with an undergraduate degree in social and political science, Harris trained at the Bristol Old Vic Theatre School. Harris is a Buddhist.

From an interview with Daily Mail: "Naomie has overcome all manner of adversity - a single-parent upbringing in North London's Finsbury Park, bullying at school, a miserable stint at Cambridge where she says she cried every day of her three-year degree course - to become one of Britain's unlikeliest celebrities.". She had a very difficult time as a student at Cambridge. "When I went to Cambridge University, Mum said I wouldn't fit in and she was right," she explains. "I hated it. The people there were so different to me. They talked about Eton and skiing and here I was, this black girl from Finsbury Park. I just felt so lone