Background: Sub-Saharan Africa (SSA) has the highest sexually transmitted infection (STI) prevalence globally, but information about trends and geographic variation is limited by sparse aetiologic studies, particularly among men. This systematic review assessed chlamydia, gonorrhoea, and trichomoniasis prevalence by sex, sub-region, and year, and estimated male-to-female prevalence ratios in SSA. Methods: We searched Embase, MEDLINE, Global Health, PubMed, and African Index Medicus for studies measuring STI prevalence among general populations from 1 January 2000, to 17 September 2024. We adjusted observations for diagnostic test performance and used log-binomial mixed-effects meta-regressions to estimate prevalence trends and sex-prevalence ratios. The study was registered with PROSPERO (CRD42023420384). Findings: Of 5202 records identified, we included 211 studies from 28 countries. In 2020, estimated prevalence among 15–49-year-olds in SSA for chlamydia was 6.9% (95% CI: 5.2–8.7%, n = 169 observations) among females and 4.2% (3.0–5.5%, n = 33) among males, gonorrhoea was 1.8% (1.1–2.5%, n = 171) and 1.5% (0.8–2.2%, n = 31), and trichomoniasis was 7.6% (5.1–10.2%, n = 188) and 1.7% (1.1–2.4%, n = 19). Male-to-female ratios were 0.61 (0.53–0.71) for chlamydia, 0.81 (0.61–1.09) for gonorrhoea, and 0.23 (0.18–0.28) for trichomoniasis. From 2010 to 2020, chlamydia prevalence increased by 34.5% (11.1–62.9%) in SSA, while gonorrhoea and trichomoniasis trends were not statistically significant. Chlamydia and gonorrhoea prevalence were highest in Southern and Eastern Africa, whereas trichomoniasis was similar across sub-regions. Interpretation: SSA has a high, geographically varied STI burden, with increasing prevalence of chlamydia. Region-specific sex-prevalence ratios differed from existing global ratios and should be considered in future burden estimates. Enhanced sex-stratified surveillance is crucial to guide national programmes and reduce STI prevalence in SSA. Funding: Gates Foundation, Imperial College London, NIH, UKRI.