Winterson was born in Manchester and adopted by Constance and John William Winterson on 21 January 1960. She grew up in Accrington, Lancashire, and was raised in the Elim Pentecostal Church. Intending to become a Pentecostal Christian missionary, she began evangelising and writing sermons at age six.
By the age of 16 Winterson had identified herself as a lesbian and left home. She soon after attended Accrington and Rossendale College, and supported herself at a variety of odd jobs while reading English at St Catherine's College, Oxford.