Charlotte Angas Scott was born on June 8, 1858, in Lincoln, England, into a Congregationalist family. At the time, the Congregationalist Church was one of the few churches to champion women's rights, in a society where girls generally received only enough education to become good wives and mothers. Women were believed to lack the intellectual capacity to attain the same level as men; in any case, such study was thought to damage their health and destroy their "feminine qualities."
At the time, no institution of higher education in the United Kingdom admitted women, and very little secondary education was available to girls. Charlotte's father, a Congregationalist minister who became president of Lancashire Independent College, a university-level institution, arranged for her to have excellent tutors, particularly in mathematics. This education, together with Charlotte's exceptional abilities, enabled her to enter Girton College in 1876. Recently founded by Emily Davies (1830–1921) as "a College like a man's" ("a college like those for men"), Girton was the first college in England to offer women higher education. In 1873, Girton students secured permission from University of Cambridge professors to attend 22 of 34 courses; later, under certain conditions, they were allowed to sit some examinations, including the famous Tripos, but could not receive a degree even if they passed. Women would not be admitted as full members of Cambridge until 1948. In 1976, Girton College became England's first women's college to admit men.
Following her success in the Tripos, Charlotte became a lecturer at Girton. This also enabled her to attend the lectures of Arthur Cayley (1821–1895), who had noticed her and would support her to the very end. In 1885, she became the first British woman to earn a doctorate, awarded by the University of London, which had begun granting degrees to women.