Objectives: This study aimed to determine the prevalence and correlates of sexual intercourse among junior secondary and high school students in Indonesia from the 2015 Global School-based Health Survey (GSHS). Methods: The survey was conducted among 11 110 students from 75 schools in Indonesia using a self-administered questionnaire. Univariate and multivariate analyses were conducted to explore associations between sexual intercourse and socio-demographic variables, substance use, mental distress, and protective factors. Results: Overall, 5.3% of students reported having ever had sex (6.9% of boys and 3.8% of girls). Of students who engaged in sexual intercourse, 72.7% of boys and 90.3% of girls had an early sexual debut (before reaching the age of 15) and around 60% had multiple sex partners. Sexual intercourse was associated with gender, school grade, smoking, alcohol consumption, drug use, suicidal ideation, truancy, peer support, and parental supervision. Conclusions These findings indicate a pressing need to develop more comprehensive sexual health education in the national curriculum. An effective strategy should also address other risky behaviours.