Fewer women than men pursue careers in science, technology, engineering and mathematics (STEM), despite girls outperforming boys at school in the relevant subjects. According to the ‘variability hypothesis’, this over-representation of males is driven by gender differences in variance; greater male variability leads to greater numbers of men who exceed the performance threshold. Here, we use recent meta-analytic advances to compare gender differences in academic grades from over 1.6 million students. In line with previous studies we find strong evidence for lower variation among girls than boys, and of higher average grades for girls. However, the gender differences in both mean and variance of grades are smaller in STEM than non-STEM subjects, suggesting that greater variability is insufficient to explain male over-representation in STEM. Simulations of these differences suggest the top 10% of a class contains equal numbers of girls and boys in STEM, but more girls in non-STEM subjects.