The purpose of this study is to evaluate the efficacy and safety of novel oral anticoagulant (NOAC) versus warfarin therapy in patients undergoing different operations. We performed a systematic review of MEDLINE, EMBASE, Cochrane Controlled Trials Register, and reports presented at scientific meetings. The efficacy and safety of NOACs during the perioperative period was compared to that using warfarin. Of the 2652 studies initially reviewed, we identified 9 that included 15,880 patients for the meta-analysis. Compared to warfarin, dabigatran increased the risk of major bleeding (RR 1.37, 95% CI 1.06-1.78, P = 0.02). Apixaban (RR 0.63, 95% CI 0.40-0.99, P = 0.04) reduced thrombotic events. NOAC therapy decreased thrombotic events in patients undergoing non-cardiac surgery (RR 0.68, 95% CI 0.50-0.92, P = 0.02). Compared to warfarin, the administration of NOACs in the perioperative period has the same risk of thromboembolism and major bleeding. But patients undergoing non-cardiac surgery may benefit more from perioperative NOAC therapy. Apixaban may reduce thrombotic events and dabigatran increases the risk of major bleeding during the perioperative period.