Bullying is a global public health issue affecting youth, especially those in school. However, there is scarcity of research exploring potential gender differences in bullying victimization in Southern Africa. Thus, this study sought to determine the prevalence and correlates of bullying victimization among in-school youth in Eswatini (formerly Swaziland), and to investigate if these differ by gender. We conducted a secondary data analysis of the 2013 Eswatini Global School-based Student Health Survey and fitted gender-specific multiple logistic regression models among a nationally representative sample of 2 920 in-school youth, a majority of whom were girls (51.9%) and were aged 15-17 years (52.8%). The overall prevalence of bullying victimization was 30.4% (30.6% among girls and 30.1% among boys, p = 0.78). Results from multivariate analysis showed that for both girls and boys, those who reported being physically attacked, engaged in physical fights, who felt lonely, and who were worried about something had higher odds of experiencing bullying victimization. Girls who used marijuana and who reported low parental connectedness had higher odds of being bullied, whereas boys who were in Form 1 (Grade 8), who went hungry and who perceived their schoolmates as unkind and unhelpful had higher odds of being bullied. Therefore, anti-bullying school programs should target both boys and girls and should take into account the different correlates for the two genders.