We assessed the efficacy of an individual-based behavioral intervention on sexually transmitted infections' (STI) risk-reduction behaviors in Singapore. A randomized controlled trial of a behavioral intervention compared to usual care was conducted on sexually active heterosexual adolescents aged 16-19 years attending the only public STI clinic. The intervention included two on-site skills-based sessions targeting individual, relational and environmental influences on sexual behaviors, followed by online support. Participants were assessed at baseline and 6-month follow-up. Primary outcomes were self-reported abstinence, number of partners and consistent condom use for vaginal sex. We recruited 337 adolescents to the intervention and 351 to usual care (controls). Fifty-nine percent of intervention participants and 53% of controls completed follow-up. Young men [adjusted risk ratio (RR) 2.03; 95% CI, 1.25-3.30], but not young women, in the intervention were more likely than controls to report secondary abstinence. More non-abstinent young women in the intervention than controls kept to one partner (adjusted RR, 1.25; 95% CI, 1.04-1.50) compared to no differences in young men. There was no intervention effect on consistent condom use in both genders. Skill-based intervention can promote abstinence in young men and keeping to one partner in young women in a clinic setting.