A prospective, non-blinded, non-randomized study on 120 wart patients treated with pulsed dye laser was performed to evaluate the efficacy and safety of pulsed dye laser treatment for viral warts and to demonstrate the proper application and effective technique of this method. The overall clearance rate was 49.5%. The clearance rates of flat warts, periungual warts, plantar warts and common warts were 67.6%, 51.1%, 47.6% and 44.3%, respectively. Overall, the response rates of pediatric warts, recalcitrant warts and old warts were superior to those of adult warts, simple warts and non-old warts, respectively; however, those trends were not statistically significant. We concluded that pulsed dye laser treatment is a safe, tolerable and relatively effective treatment method for viral warts. Pulsed dye laser treatment may be a more efficacious method for flat warts and recalcitrant periungual warts, and it can be an effective modality for newly-developed warts. The highest clearance rate was noted at a fluence of 9.5 J/cm2 (P ≤ 0.05) and it is recommended that practitioners perform pulsed dye laser treatments for viral warts at the fluences of 9.0–9.5 J/cm2. A replacement of pulsed dye laser treatment should be considered unless prominent improvement is observed after three treatment sessions.