Stowe was denied entrance into the Toronto School of Medicine in 1865 and was told by its Vice Principal, "The doors of the University are not open to women and I trust they never will be." Unable to study medicine in Canada, Emily Stowe earned her degree in the United States from the homeopathic New York Medical College for Women in 1867. The same year, she returned to Canada and opened a medical practice in Toronto, on Richmond Street. Stowe gained some local prominence through public lectures on women's health and maintained a steady clientele through newspaper advertisements. In 1870, the president of the Toronto School of Medicine granted special permission to Stowe and fellow student Jennie Kidd Trout to attend classes, a requirement for medical practitioners with foreign licences. Faced with hostility from both the male faculty and students, Stowe refused to take the oral and written exams and left the school. The College of Physicians and Surgeons of Ontario granted Stowe a licence to practise medicine on July 16, 1880, based on her experience with homeopathic medicine since 1850. This licence made Stowe the second female licensed physician in Canada, after Trout. Her daughter, Augusta Stowe-Gullen, was the first woman to earn a medical degree in Canada.
Women's rights
While studying medicine in New York, Stowe met with Susan B. Anthony and witnessed the divisions within the American women's suffrage movement. Stowe also attended a women's club meeting in Cleveland, Ohio. Stowe adopted a gradualist strategy which she brought back to her work in Canada. In 1876, Stowe founded the Toronto Women's Literary Club, renamed the Canadian Women's Suffrage Association in 1883. This has led some to consider Stowe the mother of the suffrage movement in Canada. The Literary Club campaigned for improved working conditions for women and pressured schools in Toronto to accept women into higher education. In 1883, a public meeting of the Suffrage Association led to the creation of the Ontario Medical College for Women. When the Dominion Women's Enfranchisement Association was founded in 1889, Stowe became its first president and remained president until her death. As is true for many suffragists, a tension existed between Stowe's commitment to fellow women and class loyalty. In an episode that may demonstrate the dominance of the latter, Stowe broke the bond of doctor-patient confidentiality by disclosing the abortion request of a patient, Sara Ann Lovell, a domestic servant, to her employer. Stowe, however, sharply criticized the National Policy economic program in 1892. She believed that it would not help working-class Canadians and was instead a corrupt deal on behalf of major businesses. After breaking her hip at the Columbian Exposition's Women's Congress in 1893, Stowe retired from medicine. In 1896, Emily and her daughter Augusta participated in an all-female "mock parliament," in which the women considered a petition from a male delegation for the right to vote. Stowe, as the Attorney General, used the same arguments that the Canadian Parliament had levelled against female suffragists and denied the petition. Stowe died in 1903, fourteen years before Canadian women were granted the right to vote.