This study examines the link between initial school performance on subsequent learning for marginalised children in the Complementary Basic Education programme in Northern Ghana. Specifically, we focus on whether initial low performance of girls and boys differentially affects learning trajectories. Drawing on longitudinal data, we find a significant association between initial and subsequent low performance as students transit into formal education, even after taking account of other potential factors. Boys are more likely than girls to improve from low attainment as they move into formal school. As such, girls are at particular risk of maintaining low levels of learning, and therefore warrant greater support within both complementary and mainstream schooling contexts.