While female students are more successful and show more behavioural engagement at school than male students, they also report lower levels of subjective well-being. This study examines how motivational regulation interacts with school engagement in predicting subjective well-being of male and female students. In questionnaire data from a representative sample of Flemish students in the academic track (N = 3452, age 13-14) female students reported lower subjective well-being, more engagement, and more autonomous than controlled motivation compared to male students. Multilevel-analyses, carried out separately for female and male students, revealed that for both genders, subjective well-being was positively associated with engagement and negatively associated with a more controlled than autonomous motivation. For female students only, motivational regulation significantly interacted with engagement in predicting their well-being. The negative association between having more controlled than autonomous motivation and subjective well-being was less strong for female students showing higher school engagement.