Introduction: To evaluate the intermediate-term outcomes of thulium vapoenucleation of the prostate (ThuVEP) and thulium vaporesection of the prostate (ThuVaRP) in patients with benign prostate obstruction (BPO). Materials and Methods: A bicentric retrospective matched-paired comparison of patients treated by ThuVEP (n = 80) or ThuVaRP (n = 80) was performed. The patients were preoperatively assessed with International Prostate Symptom Score (IPSS), quality of life (QoL), post-void residual urine (PVR), maximum urinary flow rate (Qmax), prostatespecific antigen (PSA) and re-evaluated at 12- and 24-month follow-up. Results: Median prostate volume was 65 mL and not different between the groups. The immediate re-operation rate was significantly different between ThuVEP and ThuVaRP (5 vs. 0%, p ≤ 0.0434). IPSS, QoL, Qmax and PVR had improved significantly compared to preoperative assessment in both groups at 12- and 24-month follow-up (p ≤ 0.001). Median Qmax (18.2 vs. 21.0 mL/s) and PVR (29.4 vs. 0 mL) were significantly different between ThuVEP and ThuVaRP at 24-month follow-up (p ≤ 0.001), while IPSS and QoL showed no differences between the groups. However, the PSA reduction was significantly higher after ThuVEP compared to ThuVaRP (78.93 vs. 23.39%, p ≤ 0.006) at 24-month follow-up. Conclusions: ThuVEP and ThuVaRP are safe and efficacious procedures for patients with BPO. Although the peri-operative re-intervention rates were lower after ThuVaRP, the low PSA reduction rate after ThuVaRP at 24-month follow-up favours the ThuVEP procedure.