Abstract Background Rifampin is recommended as adjunctive therapy for patients with a Staphylococcus aureus prosthetic joint infection (PJI) managed with debridement, antibiotics, and implant retention (DAIR), with no solid consensus on the optimal duration of therapy. Our study assessed the effectiveness and optimal duration of rifampin for S aureus PJI using Veterans Health Administration (VHA) data. Methods We conducted a retrospective cohort study of patients with S aureus PJI managed with DAIR between 2003 and 2019 in VHA hospitals. Patients who died within 14 days after DAIR were excluded. The primary outcome was a time to microbiological recurrence from 15 days up to 2 years after DAIR. Rifampin use was analyzed as a time-varying exposure, and time-dependent hazard ratios (HRs) for recurrence were calculated according to the duration of rifampin treatment. Results Among 4624 patients, 842 (18.2%) received at least 1 dose of rifampin; 1785 (38.6%) experienced recurrence within 2 years. Rifampin treatment was associated with significantly lower HRs for recurrence during the first 90 days of treatment (HR, 0.60 [95% confidence interval {CI}, .45–.79]) and between days 91 and 180 (HR, 0.16 [95% CI, .04–.66]) but no statistically significant protective effect was observed with longer than 180 days (HR, 0.57 [95% CI, .18–1.81]). The benefit of rifampin was observed for subgroups including knee PJI, methicillin-susceptible or -resistant S aureus infection, and early or late PJI. Conclusions This study supports current guidelines that recommend adjunctive rifampin use for up to 6 months among patients with S aureus PJI treated with DAIR.