Annie Nathan was born in New York City. Her sister Maud Nathan became a suffragist and social activist, and her nephew Robert Nathan became a poet and author. Annie's father suffered financial losses on Wall Street and moved the family to the Midwest; after her mother died in in 1878, the children went back to New York to live with their grandmother.
Annie was self-educated, and tutored herself in preparation for college. In 1885, she enrolled in the new course for women at Columbia College, which did not officially admit female students. After about a year, she dropped out to marry Alfred Meyer, a physician.
Annie Nathan Meyer recruited 50 well-known New Yorkers to a committee to with the goal of founding a women's college at Columbia. Barnard College opened its doors for women in a rented brownstone on Madison Avenue in September 1889. Annie Nathan Meyer became a trustee of Barnard College and was active in that position until 1942. She was also a prolific writer, producing 26 plays, three novels, an autobiography entitled It's Been Fun (1951), and two books of nonfiction, as well as newspaper and magazine articles. She also served as associate editor of the Broadway Magazine. Many of her works explored the difficulties for women of having both marriage and a career.