IMPORTANCE: Extreme precipitation, including heavy rains and flooding, is associated with poor health outcomes mediated in part by decreases in income and food production. However, the association between heavy rains and HIV burden is unknown. OBJECTIVE: To investigate the association between heavy rainfall, HIV prevalence, and HIV transmission risk over a 12-year span in sub-Saharan Africa. DESIGN, SETTING, AND PARTICIPANTS: A cross-sectional population-based study, using data collected from the 2005-2017 Demographic and Health Surveys, was conducted in 21 countries in sub-Saharan Africa and analyzed from July 29, 2021, to June 14, 2022. EXPOSURES: Heavy rainfall was defined based on the extent to which annual rainfall deviated from the historical average (standardized precipitation index ≥1.5) at the enumeration area level. MAIN OUTCOMES AND MEASURES: HIV, self-reported sexually transmitted infections (STIs), and number of sexual partners. RESULTS: The study included 288 333 participants aged 15 to 59 years; 172 344 were women (59.8%), and 183 378 were married (63.6%). Mean (SD) age was 31.9 (10.0) years. Overall, 42.4% of participants were exposed to at least 1 year of heavy rainfall in the past 10 years. Each year of heavy rainfall was associated with 1.14 (95% CI, 1.11-1.18) times the odds of HIV infection and 1.11 (95% CI, 1.07-1.15) times the odds of an STI in the past 12 months. There was also an association between heavy rainfall and the reported number of sexual partners (incident rate ratio, 1.12; 95% CI, 1.10-1.15). The odds were greater for the association between heavy rainfall and HIV prevalence and STIs among participants aged older than 20 years and participants in rural areas. CONCLUSIONS AND RELEVANCE: The findings of this study suggest that heavy rainfall was associated with a higher HIV burden in sub-Saharan Africa. The association between heavy rainfall and STIs and number of sexual partners suggests that an increase in the risk of sexual transmission is a plausible mechanism for the observed findings around HIV prevalence. Heavy rainfall could also worsen food insecurity, increasing the risk of transactional sex, or cause damage to public health infrastructure, reducing access to STI education, HIV testing, and treatment.