Ablative fractional laser (AFL)-assisted methyl aminolevulinate (MAL) photodynamic therapy (PDT) (AFL-MAL-PDT) has shown significantly higher efficacy and lower recurrence rates at 12months than conventional methyl aminolevulinate photodynamic therapy (MAL-PDT) for the treatment of Bowen disease (BD). However, long-term follow-up data are not available. To compare the 5-year efficacy and recurrence rates of AFL-MAL-PDT with those of conventional MAL-PDT for the treatment of lower extremity BD. A total of 60 patients with 84 BD lesions were randomly assigned to a single session of AFL-MAL-PDT or 2 sessions of MAL-PDT with a 1-week interval between sessions. Patients were followed up at 3, 12, 24, 36, 48, and 60months after treatment. Efficacy, recurrence rates, and risk factors for unsuccessful treatments were assessed. After 5years, the overall clearance rate of AFL-MAL-PDT (84.78%) was significantly better than that of MAL-PDT (44.74%) for BD lesions. The recurrence rate was significantly lower for AFL-MAL-PDT (9.3%) than for MAL-PDT (41.38%). Diameters larger than 20mm and lesions with a history of previous treatment were independent factors for treatment failure. The small sample size and single-center study design were limitations. For patients with lower extremity BD lesions, AFL-MAL-PDT showed significantly higherlong-term efficacy and lower recurrence rates than standard MAL-PDT.