Gender parity in academia remains elusive, even in fields, such as biological sciences, that award approximately half of their PhDs to women. Based on a sample of graduate students in biological sciences followed over 5 years during their PhD programs, we find that women publish in journals with lower impact factors and are less likely to publish in top journals. Notably, gender inequality in journal impact factors holds only for total publications but not for first-authored publications, which implies that differential opportunities for collaborations leading to high-impact publications may be one factor hindering gender equity.