A health education program conducted in primary schools in Soroti district, Uganda promoted increased access to information, better peer interactions and better quality of the health education system. A cross-sectional survey was conducted among students in their final year of primary school (average age 14 years) at baseline and two years after introduction of the intervention. The percentage of sexually active students decreased from 42.9% (123 out of 287) to 11.1% (31 out of 280) in the intervention arm, while no changes were observed in the control arm. These changes were significant, even after adjusted for gender and rural/urban location. Intervention group students were also more at ease speaking to peers and teachers about sexual issues. This type of program that emphasizes open communication and interaction can be effective in increasing abstinence among school-going adolescents in Uganda. This approach does not have to be expensive and can be done with staff already present throughout the country.