Gender is an important factor in child development. Especially in sub-Saharan Africa, girls have often been shown to be less likely to access education compared to boys. The consequence of this has been that that programmes addressing child development are often aimed at girls in order to redress gender imbalances. This study examines the effect of gender on the development of children attending community-based organisations in high HIV-affected areas, and explores whether community-based organisation attendance was associated with any changes in gender differences over time. Baseline data from 989 children and 12-15 month follow from 854 (86% response rate) were used to examine gender differences in children from Malawi and South Africa. At baseline, where there were differences by gender, these tended to disadvantage boys. It was found that boys were significantly more often found to be subjected to violence. Boys showed worse performance at school and more behavioural problems than girls. These gender differences persisted from baseline to follow-up. At follow-up, boys self-reported significantly worse average quality of life than girls. Only harsh discipline differed by gender in progression over time: boys experienced a stronger reduction in harsh physical discipline than girls from baseline to follow-up. Since harsh discipline was associated with boys’ worse educational outcomes and behavioural problems, our data cautiously suggests that gender differences could be reduced over time. In conclusion, our data suggests that, perhaps due to the narrow equity approach focusing on provision for girls, boys may be overlooked. As a result, there are some specific experiences where boys are generally worse off. These differences have distinct ramifications for the educational and emotional development of boys. A broader equity approach to child development might be warranted to ensure that the needs of both girls and boys are considered, and that boys are not overlooked.