The success of endodontic treatment is dependent on the removal of bacteria. A modern strategy to reduce bacterial load is laser irradiation. During this procedure, there is a local increase in temperature with possible side effects. The aim of this study was to determine the thermal behavior of a maxillary first molar when performing the conventional irradiation technique using a diode laser. For this study, a 3D virtual model of a maxillary first molar was created. The preparation of the access cavity, the rotary instrumentation of the palatal root canal and the laser irradiation protocol were simulated. The model was exported in a finite element analysis program where the temperature and heat flux were studied. Temperature and heat flux maps were obtained, and the temperature increase on the internal wall of the root canal was analyzed. The maximum temperature value exceeded 400 °C and was maintained for less than 0.5 s. The obtained temperature maps support the bactericidal effect of diode laser and the limitation of damage to surrounding tissues. On internal root walls, the temperature reached several hundred degrees Celsius, but for very short durations. Conventional laser irradiation is an adjuvant method of decontamination of the endodontic system.