Whitney became director of the Vassar College Observatory, succeeding her mentor Maria Mitchell.
In 1888, following the retirement of the pioneering astronomer Maria Mitchell, Mary Watson Whitney was appointed Director of the Vassar College Observatory and Professor of Astronomy. This was an extraordinary achievement for a woman in American science at the time, as directorships of major observatories were almost exclusively held by men.
Whitney had studied under Mitchell as one of her earliest students at Vassar and had spent years developing her own credentials, including advanced study of celestial mechanics under Benjamin Peirce at Harvard (informally, since women could not officially enroll) and further training in Zurich, Switzerland, where she studied with mathematician Wilhelm Fiedler.
As director, Whitney transformed the observatory into a center of serious scientific research rather than solely a teaching facility, emphasizing rigorous mathematical astronomy including the study of variable stars, comets, asteroid orbits, and double stars. She trained more than 100 women during her 22-year tenure, several of whom went on to notable careers in astronomy, continuing Mitchell's legacy of mentorship.
Her appointment and subsequent leadership helped legitimize the role of women as serious research scientists, not merely educators, and Vassar's observatory became known for producing capable women astronomers who contributed original research to the field, published in major astronomical journals of the era.