Mary Thompson may refer to:
- Mary Thompson (businesswoman) (died 1893), African American saloon and brothel owner
- Mary A. Cooke Thompson (1825–1919), women's rights activist in Oregon
- Mary Anne Thompson (1776–1852), mistress of Frederick, Duke of York
- Mary C. Thompson (died 2001), Dean of Damavand College in Tehran
- Mary Clark Thompson (1835–1923), philanthropist and wife of banker Frederick Ferris Thompson
- Mary E. Thompson (fl. 1960s–2010s), Canadian statistician
- Mary Elizabeth Thompson (1855–1953), American prostitute and dance hall girl
- Te Ata (actress) (1895–1995), born Mary Frances Thompson
- Mary Gabrielle Thompson (born 1948), Australian politician
- Mary Harris Thompson (1829–1895), founder, head physician and surgeon of the Chicago Hospital for Women and Children
- Mary Jean Thompson (fl. 1990s–2020s), American honorary consul
- Mary Wilson Thompson (1866–1947), Delaware civic leader