Although there have been some reports about the cytotoxic effects of photodynamic therapy (PDT) on multidrug-resistant bacteria, there have been few reports in which favorable results of PDT on a local infection site are described. This study aimed to verify the hypothesis that the low efficacy of PDT on a local infection site is due to the cytotoxic effect of PDT on leukocytes. PDT using Photofrin exerted significant cytotoxicity for cultured methicillin-resistant Staphylococcus aureus (MRSA). Nevertheless, this therapeutic modality was not effective for a murine MRSA arthritis model. Approximately 30% of intra-articular leukocytes, mainly neutrophils, died immediately after PDT, and a further decrease in the number of intra-articular leukocytes and atrophy of the synovial tissue were seen 24 h after PDT. Isolated peripheral neutrophils showed significant affinity for Photofrin and showed significant morphological damage, resulting in cell death, when they were subject to PDT using Photofrin. These results indicate that intra-articular neutrophils have an influence on the effects of PDT for MRSA arthritis.