Aim Perineal wound complications after abdominoperineal resection (APR) have become a major clinical challenge. Myocutaneous flap closure has been proposed in place of primary closure to improve wound healing. We conducted this comprehensive meta‐analysis to evaluate the current scientific evidence of primary closure vs myocutaneous flap closure of perineal defects following APR for colorectal disease. Methods We systematically searched the MEDLINE, Embase, PubMed, Web of Science and Cochrane Library databases to identify all relevant studies. After data extraction from the included studies, meta‐analysis was performed to compare perioperative outcomes of primary closure and myocutaneous flap closure. Results Eighteen studies with a total of 17 913 patients (16 346 primary closure vs 1567 myocutaneous flap closure) were included. We found that primary closure was significantly associated with higher total perineal wound complications (P = 0.007), major perineal wound complications (P < 0.001) and perineal wound infection (P = 0.001). On the other hand, myocutaneous flap closure takes more operation time (P < 0.001) and increases the risk of perineal wound dehiscence (P = 0.01), deep surgical site infection (P < 0.001), enterocutaneous fistulas (P = 0.03) and return to the operating room (P = 0.0005). There were no significant differences between the two groups for other outcomes. Conclusions This is the first systematic review with meta‐analysis comparing primary closure with myocutaneous flap closure of perineal defects after APR for colorectal disease. Although taking more operation time and an increased risk of specific complications, the pooled results have validated the use of myocutaneous flaps for reducing total/major perineal wound complications. More investigations are needed to draw definitive conclusions on this dilemma.