Objective This study aimed to evaluate the efficacy of beraprost sodium (BPS) or clopidogrel (CL) using vascular thromboembolic events (VTEs) of arteriovenous fistula as a primary endpoint in patients with end-stage renal disease (ESRD) undergoing arteriovenous fistula surgery. Methods We performed a multicentre, retrospective cohort study from August 2012 to August 2016. We studied patients with ESRD who underwent arteriovenous fistula surgery and received peroral administration of 40 mu g BPS, three times per day, for 1 month, or 75 mg CL (initial dose of 300 mg), one time per day, for 1 month. The time to first on-study VTE was the primary endpoint. Results The BPS-treated cohort had a significantly delayed time to first VTE compared with the CL-treated cohort (hazard ratio 0.33, 95% confidence interval 0.18-0.56). An increased incidence of VTEs was detected in the 1-month follow-up, with rates of 2.4% and 8.7% for BPS and CL, respectively. This difference persisted over time, with rates of 8.0% and 18.1% at the final follow-up, respectively. Conclusion CL-treated patients with ESRD have a greater risk of VTEs compared with BPS-treated patients. CL-treated patients also tend to experience a VTE within the first month after cessation of oral administration.