Although the perceived compatibility between one’s gender and science, technology, engineering, and mathematics (STEM) identities (gender-STEM compatibility) has been linked to women’s success in STEM fields, no work to date has examined how the stability of identity over time contributes to subjective and objective STEM success. In the present study, 146 undergraduate female STEM majors rated their gender-STEM compatibility weekly during their freshman spring semester. STEM women higher in gender rejection sensitivity, or gender RS, a social-cognitive measure assessing the tendency to perceive social-identity threat, experienced larger fluctuations in gender-STEM compatibility across their second semester of college. Fluctuations in compatibility predicted impaired outcomes the following school year, including lower STEM engagement and lower academic performance in STEM (but not non-STEM) classes, and significantly mediated the relationship between gender RS and STEM engagement and achievement in the 2nd year of college. The week-to-week changes in gender-STEM compatibility occurred in response to negative academic (but not social) experiences.