BackgroundAcute pancreatitis is a severe complication of endoscopic retrograde cholangiopancreatography (ERCP). Previous meta-analyses have shown that indomethacin effectively prevents this complication; however, the data are limited. We performed a systematic review and meta-analysis to clarify the applications for rectal indomethacin.MethodsA systematic search was performed in June 2016. Human prospective, randomized, placebo-controlled trials that compared rectally administered indomethacin with a placebo for the prevention of post-ERCP pancreatitis (PEP) were included. A meta-analysis was performed using a random-effects model to assess the outcomes (PEP) using Review Manager 5.0.ResultsSeven randomized controlled trials met the inclusion criteria (n = 3013). The overall incidence of PEP was significantly lower after prophylactic administration of rectal indomethacin than after administration of the placebo (RR, 0.58, 95% CI, 0.40–0.83; P = 0.004). A subgroup analysis was performed for rectal indomethacin administration compared to a placebo in high-risk patients (RR, 0.46; 95% CI, 0.32–0.65; P < 0.00001) and average-risk patients (RR, 0.75; 95% CI, 0.46–1.22; P = 0.25) and for administration before ERCP (RR, 0.56; 95% CI, 0.39–0.79; P = 0.001) and after the procedure (RR, 0.61; 95% CI, 0.26–1.44; P = 0.26).ConclusionsThis meta-analysis indicated that prophylactic rectal indomethacin is not suitable for all patients undergoing ERCP but it is safe and effective to prevent PEP in high-risk patients. In addition, rectal indomethacin administration before ERCP is superior to its administration after ERCP for the prevention of PEP.Electronic supplementary materialThe online version of this article (doi:10.1186/s12876-017-0599-4) contains supplementary material, which is available to authorized users.