BackgroundComprehensive sexual reproductive health (SRH) programs for female sex workers (FSW) offering clinical, behavioural, and structural interventions have contributed to declining rates of HIV in this population. However, data on costs and cost drivers is needed to support programs and their donors to better allocate resources, make an investment case for continued funding, and to identify areas of improvement in program design and implementation. We aimed to estimate the annual per-FSW costs of comprehensive services for a standalone FSW program in Kenya.MethodsWe implemented a top–bottom and activity-based costing study of comprehensive FSW services at two drop-in centres (DICs), Mtwapa and Kilifi town, in Kilifi County, Kenya. Service costs were obtained from routinely collected patient data during FSW scheduled and unscheduled visits using Kenyan Ministry of Health records. Costing data were from the program and organization’s expenditure reports, cross checked against bank documents and supported by information from in-depth interviews. Data were collected retrospectively for the fiscal year 2019. We obtained approval from the AMREF Research Ethics Committee (AMREF-ESRC P862/2020).ResultsIn 2019, the unit cost of comprehensive services was 105.93 USD per FSW per year, roughly equivalent to 10,593 Kenya shillings. Costs were higher at Mtwapa DICs compared to Kilifi town DIC; 121.90 USD and 89.90 USD respectively. HIV counselling and testing cost 63.90 USD per person, PrEP was 34.20 USD and family planning was 9.93 USD. Of the total costs, staff salaries accounted for about 60%. Adjusted for inflation, costs in 2024 would be approximately 146.60.ConclusionPrograms should strive to maximize the number of FSW served to benefit from economies of scale. Given that personnel costs contribute most to the unit costs, programs should consider alternative designs which reduce personnel and other costs.