Purpose <p>To compare the efficacy, safety and operational efficiency of radiofrequency-based transperineal thermal prostate ablation (TTPA) and single fiber transperineal laser ablation (TPLA) in patients with benign prostatic hyperplasia (BPH).</p> Materials and Methods <p>Patients with moderate to severe lower urinary tract symptoms were included and divided into TTPA and TPLA groups. Changes in International Prostate Symptom Score (IPSS), quality of life (QoL), prostate volume (PV), post-void residual (PVR), and peak urine flow rate (Qmax) at 6 and 12&#xa0;months were analyzed and compared between the two groups. Postoperative complications, operation time, ablation time were compared between the two groups.</p> Results <p>Thirty-six patients (20 TTPA vs 16 TPLA) were analyzed. At 12&#xa0;months, the between-group difference in change in IPSS, QoL, PV, Qmax and PVR from baseline was − 1.59 (95% CI: − 5.12 to 1.94, <i>p</i> = 0.37), 0.16 (95% CI: − 0.39 to 0.70, <i>p</i> = 0.57), − 5.00 (95% CI: − 10.41 to 0.41, <i>p</i> = 0.07), − 0.10 (95% CI: − 3.52 to 3.32, <i>p</i> = 0.95), − 6.40 (95% CI: − 93.30 to 81.09, <i>p</i> = 0.88). The TTPA group had significantly shorter operation time and ablation time than the TPLA group (<i>p</i> &lt; 0.001). Complication rates were similar in both groups (20% in TTPA and 25% in TPLA, <i>p</i> = 0.740), mainly urinary retention.</p> Conclusion <p>Both TTPA and TPLA effectively improved lower urinary tract symptoms in BPH patients, with no significant statistical difference in therapeutic efficacy observed at 12&#xa0;months post-procedure. TTPA was associated with a shorter operation time and ablation time, which may make it a new option for BPH treatment.</p> Level of Evidence <p>Level 3b, Retrospective Cohort Study</p> Graphical abstract <p></p>