Background Benin is among the pioneering countries that prioritised HIV prevention for female sex workers (FSWs) early on. Interventions were scaled-up, but since 2008, indicators of coverage are far from satisfactory.

Objective To better understand implementation and how to render service delivery for FSWs efficient and effective.

Methods Quantitative and qualitative methods were utilised to collect data for 2010–2011 in nine regions of Benin. A conceptual framework based on an evaluative approach was used to analyse the technical efficiency of the implementation of ongoing interventions. The Avahan (in India) and SIDA-3 (in West Africa) projects served as benchmark comparison for the programme design and implementation modalities. A top-down approach cost analysis reviewed costs in four categories: NGO activities, clinical, monitoring, and management. The output is the number of FSWs seeking STI care at user-friendly STI Clinics (SCs).

Results Allocation of funds was not proportionate to FSW needs across regions. Only 5 of 41 SCs were fully functional. Free condom distribution covers only 10% of needs. Funding gaps resulted in extended interruptions of services. The NGO cost per FSW seeking STI care varied from US$7 to more than US$2435 from one SC to the other, with an overall of US$61 per FSW visit. In high-volume SCs, the overall NGO cost per FSW visit was US$28.5 (range: US$7- US$103. This was significantly lower than in low-volume clinics (p = 0.039), where the overall NGO cost per FSW visit was US$481.7 (range: US$113-US$2435. The average total cost (NGO, clinical, surveillance and management) per FSW visit to two high-volume SCs were between US$28.6 and US$46.9, similar to the unit costs of the Avahan project.

Conclusion The study revealed deficiencies in programme design and implementation. A national framework defining an appropriate mix of interventions, management structure and operational standards is required to guide rigorous implementation.