She continued to work at the museum, largely unaided, and after 28 years, she was promoted to assistant curator in charge of the Division of Crustacea. In 1915, after her retirement, the Smithsonian Institution designated Rathbun an "Honorary Research Associate", and in 1916 she was granted an honorary master's degree by the University of Pittsburgh. She qualified for a Ph.D. at George Washington University in 1917. Rathbun was a member of the American Association for the Advancement of Science, the Washington Academy of Sciences, and the Wild Flower Preservation Society.