Improved understanding of refugees’ perceptions of provision of humanitarian support is important to improve design and delivery of humanitarian assistance. Refugee adolescents face a range of adversities, while the phase of displacement likely influences risk factors for adolescent refugees. However, evidence is sparse concerning perceptions of the impact of these factors on health and well-being of adolescent refugees. We conducted a qualitative study in November 2016, in two refugee settlements in Uganda experiencing a major influx of new refugees from South Sudan. We sought to explore one potential influence on adolescent well-being: the impact of the new influx of refugees from South Sudan on protection risks and well-being of adolescents already settled in Uganda. Themes that emerged indicate that caregivers and adolescents perceived the influx as directly impacting access to basic needs, which had direct and indirect impacts on adolescent psychosocial well-being.