She began her studies at a nearby school, then transferred to Fort Edward Institute, New York which offered college preparatory classes among others.

[3][4] During this time she spent one year in an internship at the New York Infirmary for Women and Children, which was founded by physicians Emily and Elizabeth Blackwell.

[1]: pp.15–16 Upon graduating from the New England Female Medical College, Thompson moved to Chicago, a city which had been founded only 30 years prior and with little competition for a woman physician.

In May, 1865, the Chicago Hospital for Women and Children opened, and Thompson became chief surgeon and physician, and head of staff – positions she kept the rest of her life.

[12] Thompson's private practice as an abdominal and pelvic surgeon was part of her hospital work, and for years she was the sole woman performing major surgery in Chicago.

In 1873, the Relief Aid Society of Chicago donated $25,000 to reopen the hospital and treat patients, and Thompson used the money to open in a new location that same year.

[8][12] In 1905, the hospital board gave the Art Institute of Chicago a marble sculpture titled Bust of Mary Harris Thompson that they commissioned from sculptor Daniel Chester French.