Theoretical simulations of temperature elevations in root dentin are performed to evaluate, how heating protocols affect the efficacy of using erbium, chromium; yttrium, scandium, gallium, garnet (Er,Cr;YSGG) pulsed lasers for bacterial disinfection during root canal treatments. The theoretical models are generated based on microcomputer tomography (microCT) scans of extracted human teeth. Heat transfer simulations are performed using the Pennes bioheat equation to determine temperature distributions in tooth roots and surrounding tissue during 500 mW pulsed Er,Cr;YSGG laser irradiation on the root canal for eradicating bacteria. The study not only determines the heat penetration within the deep dentin but also assesses potential thermal damage to the surrounding tissues. Thermal damage is assumed to occur when the tissue is subject to a temperature above at least 47 °C for a minimum duration of 10 s. Treatment protocols are identified for three representative tooth root sizes that are capable of maintaining elevated temperatures in deep dentin necessary to eradicate bacteria, while minimizing potential for collateral thermal tissue damage at the outer root surfaces. We believe that the study not only provides realistic laser heating protocols for various tooth root geometries but also demonstrates utility of theoretical simulations for designing individualized treatments in the future.