The fracture of nickel–titanium (Ni-Ti) instruments during root canal instrumentation leads to compromised outcomes in endodontic treatments. Despite the significant impact of instrument facture during a root canal treatment, there is still no universally accepted method to address this complication. Several previous studies have shown the ability of a Neodymium: Yttrium–Aluminum–Perovskite (Nd: YAP) laser to cut endodontic files. This study aims to determine safe irradiation conditions for a clinical procedure involving the use of a Neodymium: Yttrium–Aluminum–Perovskite (Nd: YAP) laser for removing fractured nickel–titanium files in root canals. A total of 54 extracted permanent human teeth (n = 54) were used. This study involved nine distinct groups, each employing different irradiation conditions. Groups 1 s, 3 s, 5 s, 10 s, and 15 s simply consist of irradiation for 1, 3, 5, 10, and 15 s, respectively. After identifying the longest and safest duration time, four additional groups were proposed (labeled A, B, C, and D). Group A was composed of three series of irradiations of 5 s each separated by a rest time of 30 s (L5s + 30 s RT). Group B consisted of three series of irradiations of 5 s each separated by a rest time of 60 s (L5s + 60 s RT). Group C consisted of two series of irradiations of 5 s each separated by a rest time of 30 s (L5s + 30 s RT), and group D consisted of two series of irradiations of 5 s each separated by a rest time of 5 s (L5s + 5 s RT). In all groups, during the rest time, continuous irrigation with 2.5 mL of sodium hypochlorite (3% NaOCl) was carried out. The variation in temperature during irradiation was registered with a thermocouple during irradiation with different protocols. The mean and standard deviation of the temperature increase was noted. The calculation of the temperature was made as the Δ of the highest recorded temperature at the root surface minus (-) that recorded at baseline (37°). Additionally, scanning electron microscopy (SEM) was used after irradiation in all groups in order to assess the morphological changes in the root dentinal walls. The Nd: YAP laser irradiation parameters were a power of 3W, an energy of 300 mJ per pulse, a fiber diameter of 200 µm, a pulsed mode of irradiation with a frequency of 10 Hz, a pulse duration of 150 𝜇s, and an energy density of 955.41 J/cm2. Our results show that the safest protocol for bypassing and/or removing broken instruments involves three series of irradiation of 5 s each with a rest time of 30 s between each series. Furthermore, our results suggest that continuous irradiation for 10 s or more may be harmful for periodontal tissue.