Born in Scotland, she emigrated to Boston with her husband James Fleming at the age of 21. Her husband abandoned her during her first pregnancy, and she began work as a maid in the home of Edward Pickering, the director of the Harvard Observatory.
Pickering hired her to do clerical work at the Observatory in 1881, and she devised and utilized a system of classification of stars by their spectral signature. She cataloged more than 10,000 stars over nine years, resulting in the publication of the Draper Catalogue of Stella Spectra in 1890.
She was place in charge of dozens of women hired to do mathematical classifications and edited the observatory's publications. In 1898 she was appointed curator of astronomical photographs, and in 1906 she was elected to the Royal Astronomical Society, the first American woman to be so elected. In 1907 she published a list of 222 variable stars she had discovered.
In 1910 she published her discovery of "white dwarf star."