Despite boys’ educational underachievement, gender differences in study motivation have received little research attention. Guided by self-determination theory and the identity-based motivation model, this study investigates differences in study motivation between boys and girls, as well as within each gender. To adequately consider these within-gender differences, we investigate gender and gender typicality interactions in a sample of 6,380 Flemish seventh graders collected in 2012-2013. Results from multilevel analyses show that, in line with the educational gender gap, girls display higher levels of autonomous motivation. Furthermore, gender-typical girls score highest on autonomous motivation. Gender-typical boys score considerably lower, though they outperform self-perceived atypical boys and girls. In controlled motivation, no differences are observed between boys and girls of equal ability. Nevertheless, higher scores on gender typicality contribute to a higher sense of controlled motivation. The results are discussed in light of well-being, the need for autonomy, and gendered expectations of teachers.