Background: In the past decades, there has been a growing concern to understand why boys struggle in school. One of the turning points in students' educational trajectories likely to exacerbate boys' academic difficulties is students' enrolment in private or enriched school programmes, as boys are underrepresented in such programmes. Method: To better understand this gender imbalance, our research draws on a longitudinal design to examine whether grade 6 students' externalizing behaviours, school engagement and school grades in mathematics and language arts relate to secondary school programme attendance, among a sample size of 577 students (277 boys). Results: Path analysis showed that only language arts grades predicted enrolment in private or selective public programmes and contributed to boys' underrepresentation in these programmes. Conclusions: Such findings have important implications for understanding boys' underachievement and low persistence in school as well as to guide interventions to promote gender and overall educational equity in school.