Recently, increased attention has been focused on endoscopic disinfection after outbreaks of drug‐resistant infections associated with gastrointestinal endoscopy. The aims of this study were to investigate the bactericidal efficacy of methylene blue (MB)‐based photodynamic therapy (PDT) on Pseudomonas aeruginosa (P. aeruginosa), which is the major cause of drug‐resistant postendoscopy outbreak, and to assess the synergistic effects of hydrogen peroxide addition to MB‐based PDT on biofilms. In planktonic state of P. aeruginosa, the maximum decrease was 3 log10 and 5.5 log10 at 20 and 30 J cm−2, respectively, following MB‐based PDT. However, the maximum reduction of colony forming unit (CFU) was decreased by 2.5 log10 and 3 log10 irradiation on biofilms. The biofilm formation was significantly inhibited upon irradiation with MB‐based PDT. When the biofilm state of P. aeruginosa was treated with MB‐based PDT with hydrogen peroxide, the CFU was significantly decreased by 6 log10 after 20 J cm−2, by 7 log10 after 30 J cm−2 irradiation, suggesting significantly higher efficacy than MB‐based PDT alone. The implementation of the combination of hydrogen peroxide with MB‐based PDT through working channels might be appropriate for preventing early colonization and biofilm formation in the endoscope and postendoscopy outbreak.