BackgroundFemale sex workers (FSWs) live and work in high-risk environments, experience high levels of adversity, and have multigenerational trauma that can negatively affect their children. Yet not much is known about the prevalence of victimization (i.e., exposure to maltreatment and trauma) among children of FSWs. This study compared the prevalence of lifetime victimization among adolescents of FSWs and adolescents of non-FSWs in Gulu City, Northern Uganda.MethodsA comparative cross-sectional study was conducted among adolescents (10–17 years) enrolled in the Children of At-Risk Parents (CARP) study. This study included 147 adolescents of FSWs and 147 adolescents of non-FSWs selected for comparison in Gulu City, Northern Uganda. The adolescents of FSWs were identified through their mothers using respondent-driven sampling. Data on the residence of FSWs guided a proportionate stratified sampling of adolescents of non-FSWs. Using the Juvenile Victimization Questionnaire, we screened for 34 different types of victimization during participants’ lifetimes. Percentage point differences within groups of adolescents and comparison between adolescents of FSWs and non-FSWs were calculated using STATA version 14.1. Statistical significance was set to p < 0.05.Results99.3% of the participants experienced at least one form of lifetime victimization. The median number of lifetime victimizations was 12.4. Overall, lifetime victimization was higher among adolescents of FSWs than non-FSWs (13.4 vs. 11.5), male vs. female adolescents (13.4 vs. 11.9), and older [14–17 years] vs. younger (10–13 years) adolescents (14.0 vs. 11.7). Further, more adolescents of FSWs experienced lifetime victimization in the following domains and subdomains, all of which were statistically significant: kidnap (15.8% vs. 4.8%), emotional abuse (65.8% vs. 50.0%), emotional neglect (37.4% vs. 21.1%), physical intimidation (10.2% vs. 4.1%), relational aggression (36.4% vs. 18.4%), verbal aggression (68.7% vs. 46.9%), sexual victimization (31.3% vs. 17.7%), verbal sexual harassment (20.4% vs. 5.4%), exposure to murder scene (42.9% vs. 26.5%), witness to domestic violence (39.5% vs. 26.5%), and witness to the murder of relatives (31.3% vs. 21.1%). Conversely, more adolescents of non-FSWs experienced caregiver victimization than the adolescents of FSWs (98.0 vs. 92.5; p < 0.05).ConclusionsChildhood victimization is highly prevalent in Northern Uganda and disproportionately affects the adolescents of FSWs. Therefore, government and development partners should urgently develop policies and interventions targeting prevention, early detection, and timely management of victimization in this vulnerable population.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12887-023-04131-w.