Early childhood is a critical period to intervene for obesity, developmental and behavioural problems. Data from 1065 children in 14 Northeast Iowa Community Action Head Starts (HS) were collected between 2011 and 2018. Body mass index (BMI) and developmental scores were assessed at the beginning of each school year and compared after the first year in HS. Females showed a 3.5% decrease in BMI percentile (F = 2.46, P = 0.12, = 0.02), while males increased theirs by 4.4% (F = 7.41, P = 0.007, = 0.05). Females showed higher initial passing rates than males on the Brigance (85.9% vs 75.7%, p = 0.006), self-help (64.7% vs 49.1%, p = 0.001), but not socio-emotional outcomes. Females in HS showed a slight decrease in BMI, compared to a significant increase in males. Improvements in developmental and behavioural outcomes were similar for both. Further research should determine why such differences occurred.