Stopes attended University College, London as a scholarship student, where she studied botany and geology; she graduated with a first class B.Sc. in 1902 after only two years by attending both day and night schools. Following this, Stopes earned a D.Sc. degree from University College London, becoming the youngest person in Britain to have done so. In 1903 she published a study of the botany of the recently dried-up Ebbsfleet River. After carrying out research on Carboniferous plants at the Royal Botanic Gardens, Kew, and at University College, London, she studied the reproduction of living cycads at the University of Munich, receiving a Ph.D. in botany in 1904. Also in 1904, she was one of the first women to be elected a fellow of the Linnean Society of London. She was also Fellow and sometime Lecturer in Palaeobotany at University College, London until 1920. She held the post of Lecturer in Palaeobotany at the University of Manchester from 1904 to 1910; in this capacity she became the first female academic of that university.