Internationally, girls outperform boys in overall school performance. The gender gap is particularly large among those in at-risk groups, such as children from families at economic disadvantage. This study modeled the academic trajectories of a low-income sample of boys and girls from the Concordia Longitudinal Risk Project across the full course of schooling. Results from a multiple-group latent growth curve analysis revealed that children from this low-income sample demonstrated a significant decreasing trajectory of academic performance over time, which intensified after the transition from elementary to secondary schooling. A gender gap in academic performance emerged after the children transitioned to secondary school, with girls outperforming boys. Boys continued to experience greater academic decline than did girls across the secondary school years, and individual and family characteristics assessed in early elementary school predicted these academic trajectories. At school entry, boys showed higher levels of attention problems than did girls, which in turn predicted boys’ poorer school performance. However, boys with stronger reading skills and greater maternal school involvement during the early years of schooling were protected against declining academic performance across the secondary school years. Implications for prevention programs are discussed.