In 1868, when Cooper was nine years old, she received a scholarship and began her education at the newly opened Saint Augustine's Normal School and Collegiate Institute in Raleigh, founded by the local Episcopal diocese for the purpose of training teachers to educate the formerly enslaved and their families. The Reverend J. Brinton offered Cooper a scholarship to help pay for her expenses. According to Mark S. Giles, a Cooper biographer, "the educational levels offered at St. Augustine ranged from primary to high school, including trade-skill training." During her 14 years at St. Augustine's, she distinguished herself as a bright and ambitious student who showed equal promise in both liberal arts and analytical disciplines such as mathematics and science; her subjects included languages (Latin, French, Greek), English literature, math, and science. Although the school had a special track reserved for women – dubbed the "Ladies' Course" – and the administration actively discouraged women from pursuing higher-level courses, Cooper fought for her right to take a course reserved for men, by demonstrating her scholastic ability. During this period, St. Augustine's pedagogical emphasis was on training young men for the ministry and preparing them for additional training at four-year universities. One of these men, George A.C. Cooper, would later become her husband. He died after only two years of marriage.