This paper describes a case with a 5- year follow-up of Antimicrobial Photodynamic Therapy (aPDT) associated with long-term success in endodontic treatment in a tooth with separated instruments. The patient presented with a tooth exhibiting a periapical lesion, slight swelling, and severe pain. A radiograph revealed the presence of two separated files in the middle and apical thirds of the mesial root on a lower first molar. Attempts at bypassing were not successful. In the mesial root, instrumentation was limited to the coronal ends of the separated instruments. The apical patency could not be achieved due to the blockage of the separated files. aPDT was performed in two visits, at a 660-nm wavelength and 100 mW of power, for 90 s to a total energy of 9.0 Joules. Methylene blue solution was used as photosensitizer at concentration of 0005%. A 300-μm light diffusor was coupled to the diode laser and was inserted into the root canal 2 mm short of WL, where it was set to allow better diffusion of light. Each root canal was sealed with gutta-percha by warm vertical compaction and Pulp Canal Sealer™. After 5 years of follow-up, clear evidence of remineralization of the radiolucency and bone healing was observed. This case report suggests that the addition of aPDT to conventional endodontic treatment improved microbial disinfection leading to a successful long-term outcome.