There is a paucity of data on violence against women and girls (VAWG) during conflict in general and even less specifically on violence against adolescent girls. Based on secondary analysis of a larger study in South Sudan, this article highlights the specific experience of conflict-affected adolescent girls resident in the Juba Protection of Civilian sites. Quantitative data from a cross-sectional household survey shows the prevalence of non-partner sexual violence and intimate partner violence was high among a cohort of adolescent girls during the 2013 crisis. Quantitative and qualitative data also showed that patriarchal practices, compounded by poverty and unequal power relationships within the home, remain some of the primary drivers of VAWG even in conflict-affected settings. Prevention activities need to consider these wider underlying drivers of VAWG during times of armed conflict, as they remain key factors affecting violence against adolescent girls.