Refractory cutaneous warts are difficult to eliminate. In situ photo-immunotherapy (ISPI) is an innovative treatment concept combining local photothermal therapy (PTT) and topical immunotherapy using imiquimod. To compare the efficacy of ISPI vs topical imiquimod alone, a prospective randomized controlled trial was performed with patients suffering from refractory cutaneous warts. In both groups, approximately 50% of the skin surface containing warts was treated for 6 weeks. On the basis of topical imiquimod, ISPI includes an additional 808 nm laser irradiation. Treatment response, temperatures during irradiation and histopathologic examination were evaluated. The complete response rate in the ISPI-group (22/36, 61.1%) was significantly higher than in the imiquimod alone group (11/34, 32.4%). In the ISPI-group, the mean maximum temperature was 44.5 ± 5.1°C, and obvious lymphocytic infiltration was found in the perivasculature of the dermis. There was no recurrence or worsening in both groups during the 12-month follow-up. No obvious adverse reaction was observed. This study demonstrates that ISPI can be used as an effective and safe treatment modality for refractory cutaneous warts.