To evaluate the clinical efficacy and safety of thulium laser vapoenucleation/enucleation of the prostate (ThuEP) versus holmium laser enucleation of the prostate (HoLEP) in the management of benign prostatic hyperplasia (BPH). A systematic literature search was performed using PubMed, Embase, and Web of Science to identify eligible studies published before July 2018. Meta-analysis of extracted data was performed with RevMan version 5.3. We chose the fixed- or random-effect model to fit the pooled heterogeneity. Five eligible studies including two randomized controlled trials (RCTs) and three non-RCTs involving 1010 patients were enrolled in our meta-analysis. ThuEP provided less enucleation time when compared with HoLEP (WMD = - 7.73, 95% CI - 14.39-1.07, P = 0.02). During the 1st, 6th, and 12th months of postoperative follow-ups, statistically significant differences were found in Qmax (WMD = 2.05, 95% CI 0.52~3.58) and PVR (WMD = - 6.50, 95% CI - 7.35~- 5.66, P < 0.001) in the 1st month after the operation, also in IPSS (IPSS: WMD = - 1.29, 95% CI - 2.39~- 0.19, P = 0.02) in the 12th month after the operation. As regards other perioperative, postoperative parameters, and complication rates, we found no significant difference. Both ThuEP and HoLEP provided satisfactory micturition improvement with low morbidity after the 1st and 6th months of the operation. However, ThuEP showed higher enucleation efficacy and less intraoperative blood loss and may get a better outcome as compared to the HoLEP group in the early postoperative period with regard to Qmax/PVR and IPSS after the 1st and 12th months of the operation respectively.