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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. In situ photo‐immunotherapy (ISPI) is an innovative treatment concept combining local photothermal therapy and topical imiquimod. The effectiveness and adverse reactions of ISPI for refractory cutaneous warts were evaluated in this prospective randomized controlled trial. The complete response rate of 61.1% in the ISPI‐group was significantly higher than that of 32.4% of the IMQ‐group (P < 0.05). Photothermal therapy significantly enhanced the effectiveness of topical imiquimod without any obvious adverse reactions. [ABSTRACT FROM AUTHOR]