For decades, research and public discourse about gender and science have often assumed that women are more likely than men to “leak” from the science pipeline at multiple points after entering college. We used retrospective longitudinal methods to investigate how accurately this “leaky pipeline” metaphor has described the bachelor’s to Ph.D. transition in science, technology, engineering, and mathematics (STEM) fields in the U.S. since the 1970s. Among STEM bachelor’s degree earners in the 1970s and 1980s, women were less likely than men to later earn a STEM Ph.D. However, this gender difference closed in the 1990s. Qualitatively similar trends were found across STEM disciplines. The leaky pipeline metaphor therefore partially explains historical gender differences in the U.S., but no longer describes current gender differences in the bachelor’s to Ph.D. transition in STEM. The results help constrain theories about women’s underrepresentation in STEM. Overall, these results point to the need to understand gender differences at the bachelor’s level and below to understand women’s representation in STEM at the Ph.D. level and above. Consistent with trends at the bachelor’s level, women’s representation at the Ph.D. level has been recently declining for the first time in over 40 years.