Background Little is known regarding human immunodeficiency virus (HIV)/sexually transmitted infection (STI) testing preferences for location, staffing, and hours of operation among Young Black men who have sex with men (YBMSM) in the Southeastern United States, a population at high risk for HIV/STIs. We used a discrete choice experiment to explore these preferences. Methods Young Black men who have sex with men ages 16 to 35 years in Birmingham, AL and Jackson, MS completed online surveys evaluating their preferences (best/worst) for HIV/STI testing locations, staffing, hours, method of results notification, and cost. They also selected preferred combinations of these variables through choice tasks. Results were analyzed using joint best/worst and discrete choice experiment models. Results Between June 2018 and December 2019, participants in Alabama (n = 54) and Mississippi (n = 159) completed online surveys. Both groups preferred stationary testing locations over mobile testing vans, with the most significant difference favoring STI testing-only clinics in Mississippi and local health departments in Alabama (P < 0.001). Technician-performed tests or self-testing were significantly less preferred compared with clinician-performed testing for both groups (P < 0.0001 and P < 0.0001, respectively). Free testing and phone results notification (versus text) were preferred by both groups. The most desirable combination among all participants was weekday clinician-performed testing at the health department for $5. Conclusions Young Black men who have sex with men in the Southeastern United States prefer traditional testing locations staffed by experienced personnel. Combination choices are influenced by services that are low or no cost. More research is needed to inform the best way(s) to provide affordable, high-quality HIV/STI testing services for YBMSM, particularly in the post-COVID-19 era when sexual health care delivery models are evolving toward home-based and remote health-focused strategies.