Background Global efforts in response to the increased prevalence of the human immunodeficiency virus (HIV) are mainly aimed at reducing high risk sexual behaviors among young people. However, knowledge regarding intentions of young people to engage in protective sexual behaviors is still lacking in many countries around the world, especially in Sub-Saharan Africa where prevalence of human immunodeficiency virus is the highest. The objective of this study was to test the theory of planned behavior (TPB) for predicting factors associated with protective sexual behaviors, including sexual abstinence and condom use, among in-school youths aged between 15 and 19 years in Swaziland. Methods This cross-sectional survey was conducted using a anonymous questionnaire. A two-stage stratified and cluster random sampling method was used. Approximately one hundred pupils from each of four schools agreed to participate in the study, providing a total sample size of 403 pupils of which 369 were ultimately included for data analysis. The response rate was 98%. Structural equation modeling was used to analyse hypothesized paths. Results The TPB model used in this study was effective in predicting protective sexual behavior among Swazi in-school youths, as shown by model fit indices. All hypothesized constructs significantly predicted intentions for abstinence and condom use, except perceived abstinence controls. Subjective norms were the strongest predictors of intention for premarital sexual abstinence; however, perceived controls for condom use were the strongest predictors of intention for condom use. Conclusions Our findings support application of the model in predicting determinants of condom use and abstinence intentions among Swazi in-school youths.