Youth living in rural Uganda represent over 20% of the country’s population. Despite the size of this demographic, there is a paucity of data on their health priorities. Engaging people in understanding their own health status has been proven to be an effective mechanism for health promotion. The objective of this study was to use Photovoice, a community-based, participatory action research methodology, to understand the current health priorities of youth living in rural Uganda. Thirty-two students between the ages of 13 and 17 were recruited from four schools within the region of Soroti, Uganda. Participants were given a disposable camera and were asked to photograph situations that contributed or detracted from their health status. The cameras were then returned to the investigators and each photo taken by the participant was reviewed with the investigators during a semi-structured interview. Codes were applied to the photographs and organized into overarching themes. Each participant chose one to two photos that were most representative of their health priorities for a secondary analysis. Participants provided 499 photos that met the eligibility criteria. The most common themes presented in the photographs were ‘hygiene’ (n = 73, 12.4%), ‘nutrition’ (n = 69, 11.7%), and ‘cleanliness’ (n = 48, 8%). ‘Hygiene’ (n = 6, 14.6%) and ‘exercise’ (n = 6, 14.6%) were the most common priorities articulated in the representative photographs. Photovoice proved to be an effective method to assess and express the health concerns of youth in rural Uganda. Study participants were able to articulate their health concerns and priorities through photographs and reflect on opportunities for health promotion through subsequent interviews.