This study examined differences in sexual risk behaviors by gender and over time among 1281 patients (777 males and 504 females) from 12 community-based substance use disorder treatment programs throughout the United States participating in CTN-0032, a randomized control trial conducted within the National Drug Abuse Treatment Clinical Trials Network. Zero-inflated negative binomial and negative binomial models were used in the statistical analysis. Results indicated significant reductions in most types of sexual risk behaviors among substance users regardless of the intervention arms. There were also significant gender differences in sexual risk behaviors. Men (compared with women) reported more condomless sex acts with their non-primary partners (IRR = 1.80, 95 % CI 1.21–2.69) and condomless anal sex acts (IRR = 1.74, 95 % CI 1.11–2.72), but fewer condomless sex partners (IRR = 0.87, 95 % CI 0.77–0.99), condomless vaginal sex acts (IRR = 0.83, 95 % CI 0.69–1.00), and condomless sex acts within 2 h of using drugs or alcohol (IRR = 0.70, 95 % CI 0.53–0.90). Gender-specific intervention approaches are called for in substance use disorder treatment.