OBJECTIVE For the successful treatment of thrombosed autogenous arteriovenous fistula (AVF), we designed and performed a hybrid surgery. Its clinical outcomes were compared with those of percutaneous mechanical thrombectomy, retrospectively. METHODS Forty cases of thrombosed autogenous AVFs underwent hybrid surgery, whereas 19 cases received percutaneous mechanical thrombectomy. Hybrid surgery consisted of surgical thrombectomy, balloon angioplasty and/or additional surgical angioplasty. Percutaneous mechanical thrombectomy included catheter-introduced thrombus aspiration, balloon angioplasty and/or stenting. Procedure related outcomes such as technical success rates and primary patency rates were analyzed, retrospectively. RESULTS There were no statistically significant differences between the two groups in terms of demographic data of the patients including age, gender, diabetes status, and frequency of antiplatelet use, as well as the characteristics of thrombosed autogenous AVFs such as access age, site, type, and length of time between thrombosis and AVF creation (P > 0.05). Technical success rates (92.5% vs. 68.4%, P = 0.005, respectively) and primary patency rates (85.9% vs. 36.8% at 6 months, 81.1% vs. 26.3% at 12 months, 81.1% vs.21.1% at 18 and 24 months respectively, log-rank test, (P < 0.001) were significantly higher in the hybrid surgery group. In terms of cost analysis, supply cost was not different (P = 0.065), but total cost was statistically lower in the hybrid surgery group (P = 0.019). CONCLUSIONS Hybrid surgery showed better technical success rates and patency rates in the salvaging of thrombosed autogenous AVFs than in percutaneous mechanical thrombectomy.