Root canal therapy is a predominant method for treatment of dental pulp and periapical diseases. Conventional methods such as mechanical instrumentations, chemical irrigation and intracanal medicaments pose a huge limitation to root canal disinfection as they kill bacteria and dental stem cells simultaneously. Therefore, much attention has been focused on finding more efficacious antibacterial methods that has no or negligible cytotoxicity for dental stem cells. Herein, we hypothesized that combining antibacterial medicaments with Antimicrobial photodynamic therapy (aPDT) and methylene blue (MB) as a photosensitizer would be effective in reducing death of dental pulp stem cells (DPSCs). To examine this, DPSCs were isolated from third molar teeth through enzymatic digestion. Isolated cells were cultured in αMEM and when reached adequate confluency, were used for further analysis. Cytotoxicity effect of different groups of MB, DAP, MB, LED and their combination on DPSCs was analyzed using MTT assay. DPSCs membrane integrity as a marker of live cells was assessed through measuring lipid peroxidation and lactate dehydrogenase (LDH) release into extracellular space. Results showed that the combination of LED, MB and TAP or aPDT, MB and DAP was more effective in reducing DPSCs death rate compared to TAP and DAP administration alone. Moreover, Malondialdehyde (MDA) and LDH levels were found to be decreased in cells exposed to combination treatment in comparison with single TAP or DAP therapy. Our study shows the promising perspectives of employing combined aPDT, MB and antibiotic medicaments for reduction of dental stem cell death.