Introduction Violence against adolescents is prevalent in the world, yet this issue is neglected especially in developing countries. Bullying among adolescents negatively affects the victims in relation to emotional, physical, social and overall health status. This study was conducted to understand bullying and its associated factors in school-going adolescents in Indonesia. Methods This study was a correlational design with a cross-sectional approach. Data were obtained from the 2015 Indonesia Global School-based Health Survey (GSHS). As many as 9969 adolescents in schools were selected by probability proportional to size method and systematic sampling. Variables analyzed on this study were age, sex, smoking behavior, alcohol consumption, close friends and feeling of loneliness. The research instrument used the GSHS 2015 questionnaire. Chi-square (χ2) analysis and multiple logistic regression tests were conducted to determine the significance of each variable. Results A total of 19.9% of adolescents in Indonesian schools were victims of being bullied. Being bullied was associated with ≤14 years old [adjusted odds ratio (AOR) 1.30, 95% confidence interval (CI) 1.17-1.45], being male (AOR 1.43, 95% CI 1.28-1.59), being a smoker (AOR 1.46, 95% CI 1.23-1.73), consuming alcohol (AOR 2.07, 95% CI 1.64-2.62), having no close friends (AOR 1.27, 95% CI 0.95-1.70) and feeling lonely (AOR 2.29, 95% CI 2.05-2.55). Conclusion Indonesian in-school adolescents report a relatively high prevalence of having been bullied. Being bullied is related to various factors depending on personal and environmental factors. School communities and health professionals' attention to adolescents should be sensitized and this issue discussed, developing strategies and minimizing the negative effect on the adolescents. Policy makers need to consider developing a social platform among adolescents to facilitate students' interaction.