Background Cisgender female sex workers (FSWs) in sub-Saharan Africa have a high risk of HIV acquisition, highlighting the need for innovative approaches to expand coverage of evidence-based HIV prevention methods, including oral pre-exposure prophylaxis (PrEP). Our study aimed to identify FSWs’ preferences for a PrEP delivery model with structured choices for delivery location, services offered, and adherence support. Methods We conducted a discrete choice experiment (DCE) among FSWs ≥18 years recruited from the Most At-Risk Population Initiative (MARPI) clinic in Kampala, Uganda, between October and November 2023. FSWs were recruited using consecutive sampling. To determine the most effective PrEP delivery method for FSWs, we created eight choice sets, each with three alternative combinations of PrEP service attributes and an opt-out using a D-efficient experimental design. Participants were presented with three alternatives, the fourth being an opt-out (no model selected), and asked to make selections based on four distinct attributes: the PrEP provider, place of delivery, delivery channel, and support services. We assessed FSW preferences and attribute trade-offs using a panel data mixed model and identified the preferred PrEP delivery model using the highest median utility score. Results Overall, 203 participants completed the DCE. The median age was 24 years (interquartile range [IQR] 20-32). Most FSWs preferred receiving PrEP from a healthcare worker at the clinic with short message service (SMS) reminders for adherence support (median utility score 0.87; interquartile range [IQR] 0.82, 0.94). This preference remained consistent across all age groups, with a median utility score of 0.88 for ages 15-19, 0.87 for ages 20-24, and 0.85 for ages ≥25. Conclusion FSWs preferred to receive PrEP care directly from providers at healthcare facilities and highlighted the need for additional support in the form of SMS reminders to improve adherence and prevent HIV acquisition. This preferred model, if implemented, could increase prevention coverage and inform future approaches to delivering PrEP through the Uganda National PrEP Program.