Adolescent sexual and reproductive health problems remain a public health concern in Indonesia. An increase of premarital sex as well as early sexual debut among adolescents without any protection leads to a high risk of adverse sexual and reproductive health consequences. This study aimed to assess condom use prevalence and identify its determinants among male adolescents who are sexually active in Indonesia. This was a cross-sectional study using secondary data from the Adolescent Reproductive Health component of the Indonesia Demographic and Health Survey (IDHS) 2012. The sample for this study was 1341 sexually active male adolescents aged 15–24 years old. Data were analyzed descriptively and using binary logistic regression for bivariate and multivariate analysis. This study found that condom use prevalence among male adolescents at first and last sex accounted for 25.0% and 27.4%, respectively. Determinants of condom use varied by time of sexual intercourse. Knowledge of sexual and reproductive health and obtaining information about condoms were consistently related to condom use at first and last sexual encounter. Meanwhile, residential type, age at first sex, and sexual partner were significant determinants of condom use at sexual debut whilst educational level was only associated with condom use at last sex. As the level of protected sex among male adolescents was very low, providing comprehensive sexuality education (CSE) is suggested in order to develop the capacity among adolescents in making informed decisions and preventing unsafe sex.