Abstract Background Educational attainment is an important determinant of diverse health outcomes. Truancy among adolescents jeopardizes chances of achieving their educational goals. Truant behaviors are also associated with various psychosocial problems. There is however limited data on the prevalence and factors associated with truancy among adolescents in Africa. Methods We used data from the Swaziland Global School-Based Health Survey (GSHS) conducted in 2003 to estimate the prevalence of self-reported truancy within the last 30 days among adolescents. We also assessed the association between self-reported truancy and a selected list of independent variables using logistic regression analysis. Results A total of 7341 students participated in the study. In analysis of available data, 2526 (36.2%) and 4470 (63.8%) were males and females respectively. The overall prevalence of truancy within the last 30 days preceding the study was 21.6%. Prevalence of truancy was 27.4% (605) and 17.9% (723) in males and females respectively. In multivariate logistic regression analysis, being a male, having been bullied, lower school grades, and alcohol use were positively associated with truancy. Adolescents who perceived themselves as having parental support were less likely to have reported being truant. Conclusion Truancy among adolescents in Swaziland should be regarded as an important social problem as it is relatively prevalent. The design and implementation of intervention programs aimed to reduce truant behaviours should incorporate our knowledge of the factors identified as associated with bullying.