Controversies exist over which type of graft is best for the reconstruction of the anterior cruciate ligament (ACL). The purpose of this systematic review was to evaluate the effectiveness of ACL reconstruction using either hamstring (HT) autografts or bone-patellar tendon-bone (BPTB) autografts. We searched the Cochrane Library, MEDLINE and EMBASE for published randomized controlled trials (RCT) comparing HT autografts with BPTB autografts for ACL reconstruction. Data analyses were performed using Cochrane Collaboration RevMan 5.0. Nine RCTs (738 patients) met the inclusion criteria. The combined results of the meta-analysis indicated there was a significantly lower rate of negative Pivot test [relative risk (RR) 0.87, 95 % confidence intervals (CI) 0.79-0.96, P = 0.004], anterior knee pain (RR 0.66, 95 % CI 0.45-0.96, P = 0.03) and of kneeling pain (RR 0.49, 95 % CI 0.27-0.91, P = 0.02) in the HT group than in the BPTB group. ACL reconstruction with HT autografts or BPTB autografts achieved similar postoperative effects in terms of restoring knee joint function. HT autografts were inferior to BPTB autografts for restoring knee joint stability, but were associated with fewer postoperative complications.