Stopes was born in Edinburgh. Her Father, Henry Stopes, was a brewer, Engineer, Architect and Paleontologist from Colchester. Her mother was Charlotte Carmichael Stopes, a Shakespearean scholar and women's rights campaigner from Edinburgh. At six weeks old, her parents took Stopes from Scotland; the family stayed briefly in Colchester then moved to London, where in 1880 her Father bought 28 Cintra Park in Upper Norwood. Both of her parents were members of the British Association for the Advancement of Science, where they had met. Marie was taken to meetings where she met the famous scholars of the day. At first, she was home-schooled, but from 1892 to 1894 she attended St George's School for Girls in Edinburgh. Stopes was later sent to the North London Collegiate School, where she was a close friend of Olga Fröbe-Kapteyn.