Abstract Background and aims Patients with ulcerative colitis (UC) have an elevated thromboembolic risk. The comparative risks associated with advanced therapies (ADTs) remain unclear. Methods In this retrospective cohort study, we utilized the Japanese Medical Data Vision claims database to assess patients with UC who initiated treatment with tumor necrosis factor (TNF) inhibitors, vedolizumab, or tofacitinib. We evaluated the cumulative incidence and hazard ratios (HRs) for venous thromboembolisms (VTEs), cardiovascular events (CVEs), and major adverse cardiovascular events (MACEs). The tofacitinib dose was modeled as a time-varying covariate. Results In total, 8125 TNF inhibitor users, 1218 tofacitinib users, and 2469 vedolizumab users were analyzed. Compared with TNF inhibitors, vedolizumab was associated with a lower risk of VTE (HR ,50, 95% CI 0.30-0.81) and CVE (HR 0.47, 95% CI, 0.27-0.81), with no difference in MACE. Tofacitinib 5 mg and 10 mg administration twice daily (BID) showed no significant differences vs TNF inhibitors, though point estimates were lower at 5 mg and higher at 10 mg. Concomitant 5-aminosalicylic acid was associated with a lower incidence of VTE. Conclusions Vedolizumab demonstrated a favorable thromboembolic and cardiovascular safety profile compared with TNF inhibitors, whereas tofacitinib did not increase the risk at either dose. Concomitant 5-aminosalicylic acid may have a preventive effect against VTE. These findings may aid therapeutic decision-making for UC patients with elevated thrombotic risk.