Within weeks of her wedding, Meyer began organizing a committee to found a women's college at Columbia and provide for young women the opportunity for an education that she herself had not enjoyed. Meyer understood that the idea was nothing without funding, and created a committee of fifty prominent New Yorkers to willing to support the projected college. She overcame the opposition of the Columbia trustees with a brilliant maneuver: she named the college after F.A.P. Barnard, Columbia's recently deceased president. The college Meyer founded, Barnard College, is (one of the Seven Sisters) and ranks today as one of America's most elite colleges.
She became known as an opponent of woman suffrage (in direct conflict to her sister Maud Nathan). At one time, Annie Nathan Meyer was associate editor of the Broadway Magazine. She edited Woman's Work in America (1891) and contributed a series of articles to the New York Evening Post.