Transurethral resection of the prostate (TURP) is the gold-standard classical method for the treatment of benign prostatic hyperplasia (BPH). In minimally invasive surgery, holmium laser enucleation of the prostate (HoLEP) is considered an alternative option. In this systematic review and meta-analysis, we aimed to comprehensively evaluate the advantages and disadvantages of TURP and HoLEP the treating BPH. We comprehensively searched PubMed, Cochrane Library, EMBASE, and Web of Science databases for all randomized controlled trials published before 1 December 2022 comparing HoLEP and TURP. The study protocol is registered on INPLASY (DOI: 10.37766/inplasy2023.5.0065). Compared with TURP, HoLEP required longer operation time but shorter catheter duration, hospital stay, and bladder irrigation time, as well as less postoperative irrigation. With HoLEP, maximum urinary flow rate at 12 and 24 months after surgery; post-void residual volume at 1, 6, and 12 months; and International Prostate Symptom Score at 12 months after surgery were superior to those with TURP. HoLEP was associated with significantly lower risk of hyponatremia, blood transfusion, and urethral stricture but greater risk of postoperative dysuria. Compared with TURP, HoLEP had better curative efficacy at 6, 12, and 24 months after operation and lower incidence of adverse events in patients with BPH.