Although Mary Walker received a physician's certificate to practice medicine in 1855, when the Civil War started she was accepted only as a nurse in the military. Not until 1864 was she recognized as a qualified doctor and given a commission, but could serve only as an assistant surgeon. She was given the Medal of Honor in 1865 for her service, but a federal review board revoked the medal in 1917, claiming she never actually served in the Army. The U.S. Army restored the medal in 1977.

After the war, and a short period as a journalist, she moved to Washington, DC, to practice medicine. By day, as a physician, she wore men's attire. After working hours, she changed her dress and hair and was totally a lady. An advocate of women's rights, she lectured on the subject and demonstrated that she was capable of performing the same as any many with equal qualifications.