Kingsley was born Krishna Bhanji in Snainton, near Scarborough, Yorkshire, England, the son of Anna Lyna Mary (née Goodman), an actress and model, and Rahimtulla Harji Bhanji, a medical doctor. Kingsley's father, an Ismaili Muslim, was born in Kenya of Indian Khoja Gujarati descent, as Kingsley's paternal grandfather was a spice trader who had moved from India to Zanzibar, where Kingsley's father lived until moving to England at the age of fourteen. Kingsley's mother, born out of wedlock, was "loath to speak of her background"; she was the daughter of an English East London garment worker mother and a father who was believed by the family to have been a Russian or German Jew.

Kingsley grew up in Pendlebury, Salford, where he studied at University of Salford. He then moved to Lancashire, where he studied at Pendleton College, which later became home to the Ben Kingsley Theatre. Kingsley began his acting career on the stage at Manchester Grammar School, alongside Robert Powell,