High recurrence rate and adverse effects were common shortcomings in treatments for genital warts, but a number of clinical studies have found that photodynamic therapy (PDT) had some unique superiority compared to other treatments. This study aims to evaluate the efficacy and safety of PDT for genital warts in comparison to alternative treatments. Seven databases and http://clinicaltrials.gov were searched and seven randomized controlled trials were finally included. There was no significant difference in clearance rate of urethral lesions between the PDT group and the CO2 laser therapy (CO2‐LT group) (Odds ratio [OR] 0.676, 95% confidence interval [CI] 0.071–6.426, P = 0.734), but the overall clearance rate of all genital warts was slightly lower for PDT (OR 0.574, CI 0.335–0.985, P = 0.044). The recurrence rate after PDT was significantly lower than after CO2‐LT (OR 0.318, CI 0.220–0.460, P < 0.001), and adverse effects were also slighter after PDT (OR 0.015, CI 0.003–0.074, P < 0.001). In addition, a modification of parameters of light irradiation provides the potential to alleviate pain. This study shows that PDT is an effective treatment for genital warts with good tolerability and safety, especially for cavitary lesions. Some modified protocols probably have the potential to reduce adverse effects, but still need further investigation.