Drawing on 48 interviews with science, technology, engineering and mathematics (STEM) doctoral students at a private research university in the United States (US), we examine how students make sense of the preponderance of men at the faculty level despite increasing gender parity among students. Students’ primary explanatory frame, historical bias, suggests that the gender gap will disappear when enough women attain their doctorates (PhDs). Competing frames include innate and constructed gender difference and the perceived incompatibility between a woman’s body clock and an academic tenure clock. We argue that the frames that students use to explain the gender gap shed light on the cultural context of STEM, which is characterized by a tension between the belief in a meritocratic system and the acknowledgement of structural inequality. We suggest that men and women’s preference for explanations that preclude bias, in light of women students’ own experiences with sexism in graduate school, contributes to the reproduction of inequality by rendering invisible structural barriers to gender equality.