Background: Black sexual minority men (BSMM) and Black transgender women face a disproportionate risk of incarceration and sexually transmitted infection (STI)/HIV, yet research on the longitudinal association between incarceration and STI/HIV risk in these groups is limited. Methods: We used data from the HIV Prevention Trials Network (HPTN) 061 study conducted among BSMM and Black transgender women in Atlanta, Boston, Los Angeles, New York City, San Francisco, and Washington, DC, restricting analyses to those who returned for the 6-month follow-up visit when recent incarceration was measured (n = 1169). Using inverse probability of treatment weighting, we measured associations between incarceration and next 6-month multiple partnerships; selling or buying sex; condomless anal intercourse; and incident chlamydia, gonorrhea, syphilis, and HIV. We explored differences by study city, and among BSMM who had sex with men only, BSMM who had sex with men and women, and Black transgender women. Results: Approximately 14% reported past 6-month incarceration. Incarceration was associated with next 6-month selling sex (adjusted risk ratio [ARR], 1.80; 95% confidence interval [CI], 1.12-2.87) in the overall sample and multiple partnerships among BSMM who had sex with men and women (ARR, 1.34; 95% CI, 1.10-1.63) and transgender women (ARR, 1.77; 95% CI, 1.22-2.57). There is evidence suggesting that incarceration may predict gonorrhea (ARR, 2.35; 95% CI, 0.95-5.77), with particularly strong associations observed in Los Angeles (ARR, 6.48; 95% CI, 1.48-28.38). Conclusions: Incarceration may increase STI/HIV risk among BSMM and Black transgender women. Additional mixed-methods research is needed to validate associations and understand pathways.