The Ugandan government has been criticised on several grounds for its abstinence-only policies on sexuality education directed towards young people. These grounds include the failure to recognise the multiple realities faced by young people, some of whom may already be sexually active. In the study reported on this paper, students’ perceptions of relationships and sexual practices were analysed to obtain an understanding of how young people construct and negotiate their sexual agency in the context of abstinence-only messages provided in Ugandan secondary schools and at the wider community level. Ten in-depth interviews and six focus group discussions were conducted with students aged 15–19 years (N = 55) at an urban co-educational secondary school. Data were transcribed verbatim and analysed using grounded theory. Findings show that students engage in sexual activity despite their belief that contraception is ineffective and their fears for the consequences. Students’ age, gender, financial capital and perceived sexual desire further increase risk and vulnerability. To improve their effectiveness, school-based sexuality education programmes should support students to challenge and negotiate structural factors such as gender roles and sociocultural norms that influence sexual practices and increase vulnerability and risk.