In Uganda, women engaged in sex work (WESW) are a marginalized population at the intersection of multiple vulnerabilities. The Kyaterekera intervention is targeted at WESW in Rakai and the greater Masaka regions in Uganda and combines a traditional HIV risk-reduction approach with a savings-led economic empowerment intervention and financial literacy training. We estimated the economic costs of the Kyaterekera intervention from a program provider perspective using a prospective activity-based micro-costing method. All program activities and resource uses were measured and valued across the control arm receiving a traditional HIV risk-reduction intervention and the treatment arm receiving a matched individual development savings account and financial literacy training on top of HIV risk reduction. The total per-participant cost by arm was adjusted for inflation and discounted at an annual rate of 3% and presented in 2019 US dollars. The total per-participant costs of the control and intervention arms were estimated at $323 and $1,435, respectively, using the per-protocol sample. When calculated based on the intent-to-treat sample, the per-participant costs were reduced to $183 and $588, respectively. The key cost drivers were the capital invested in individual development accounts and personnel and transportation costs for program operations, linked to WESW's higher mobility and the dispersed pattern of hot spot locations. The findings provide evidence of the economic costs of implementing a targeted intervention for this marginalized population in resource-constrained settings and shed light on the scale of potential investment needed to better achieve the health equity goal of HIV prevention strategies.