Aims Benign prostatic hyperplasia (BPH) represents a significant public health issue in Japan. This study evaluated the lifetime cost-effectiveness of water vapor energy therapy (WAVE) versus prostatic urethral lift (PUL) for men with moderate-to-severe BPH from a public healthcare payer’s perspective in Japan. Materials and methods A decision analytic model compared WAVE to PUL among males in Japan. Clinical effectiveness and adverse event (AE) inputs were obtained from a systematic literature review. Resource utilization and cost inputs were derived from the Medical Data Vision database and medical service fee national data in Japan. Experts reviewed and validated model input parameters. One-way and probabilistic sensitivity analyses were conducted to determine how changes in the values of uncertain parameters affect the model results. Results Throughout patients’ lifetimes, WAVE was associated with higher quality-adjusted life years (0.920 vs. 0.911 year 1; 15.564 vs. 15.388 lifetime) and lower total costs (¥734,134 vs. ¥888,110 year 1; ¥961,595 vs. ¥1,429,458 lifetime) compared to PUL, indicating that WAVE is a more effective and less costly (i.e. dominant) treatment strategy across all time horizons. Lifetime cost-savings for the Japanese healthcare system per patient treated with WAVE instead of PUL were ¥467,863. The 32.7% cost difference between WAVE and PUL was predominantly driven by lower WAVE surgical retreatment rates (4.9% vs. 19.2% for WAVE vs PUL, respectively, at 5 years) and AE rates (hematuria 11.8% vs. 25.7%, dysuria 16.9% vs. 34.3%, pelvic pain 2.9% vs. 17.9%, and urinary incontinence 0.4% vs. 1.3% for WAVE vs PUL, respectively, at 3 months). Model findings were robust to changes in parameter input values. Limitations The model represents a simplification of complex factors involved in resource allocation decision-making. Conclusions Driven by lower retreatment and AE rates, WAVE was a cost-effective and cost-saving treatment for moderate-to-severe BPH in Japan compared to PUL, providing better outcomes at lower costs to the healthcare system.