Experiences of childhood violence and violence perpetration and the association with inequitable gender norms and violence justification have been extensively studied in non-humanitarian settings, and among older populations. However, there is a gap in understanding these associations within humanitarian contexts, particularly from the perspective of children and youth. We used data from the Uganda Humanitarian Violence Against Children and Youth Survey, a representative, cross-sectional household survey of 2,265 children and youth aged 13-24 years living in refugee settlements in Uganda. We explored associations between endorsement of inequitable gender norms, intimate partner violence (IPV) justification, and experiences of violence and/or perpetration of violence in childhood. Experience of any childhood violence was significantly associated with an increase in endorsement of inequitable gender norms among females and IPV justification among males. This pattern was similar for 18-24-year-olds. Among 13-17-year-olds, IPV justification was significantly associated with experience of any childhood violence among females and perpetration of violence among males. Our findings suggest the need for gender-transformative violence prevention interventions that start early in the life course, and that address inequitable gender socialisation and power relations. School-based violence prevention interventions, community-based approaches to form gender equitable attitudes among adolescents, parenting interventions, and interventions with children and adolescents that had experienced childhood violence have shown considerable success in other settings, and could be adapted to humanitarian settlements.