After her husband's death, Cooper entered Oberlin College in Ohio, where she continued to follow the course of study designated for men, graduating in 1884. Given her academic qualifications, she was admitted as a sophomore. She often attempted to take four classes, rather than three as was prescribed by the College; she also was attracted to Oberlin by its reputation for music, but was unable to take as many classes in piano as she would have wished. Among her classmates were fellow black women Ida Gibbs (later Hunt) and Mary Church Terrell. At Oberlin, she was part of the "LLS", "one of the two literary societies for women, whose regular programs featured lectures by distinguished speakers as well as singers and orchestras". After teaching briefly at Wilberforce College, Cooper returned to St. Augustine's in 1885. She then went back to Oberlin and earned an M.A. in Mathematics in 1888, making her one of the first two Black women - along with Mary Church Terrell, who received her M.A. in the same year - to earn a Master's degree.