To compare the efficiency of root canal filling removal from oval-shaped root canals with high-energy Er:YAG laser and additional instrumentation with a rotary Ni-Ti XP-Endo Finisher R system. The in vitro study was accomplished on 12 freshly extracted single-rooted mandibular incisors with one straight oval-shaped root canal, shaped with XP-Endo Shaper 30/.04 and obturated by using the warm vertical condensation technique subjected to further endodontic orthograde retreatment. Group 1: the first retreatment was carried out using a high-energy Er:YAG laser (n = 12). Group 2: the additional retreatment of the same specimens was performed with the XP-Endo Finisher-R system (n = 12). The effectiveness of the retreatment techniques was evaluated by a threefold micro-CT examination. The amount of the remaining root canal filling material was analyzed by Mann-Whitney U test and Friedman tests. A significant decrease in the quantity of the root canal filling was found following the first and after the second retreatment, compared to the initial values in all examined sections (P < 0.001). Within groups, additional application of the Ni-Ti system resulted in no significant removal of the filling materials (P > 0.05). None of the systems resulted in complete root canal filling removal. Despite the improved results after the application of the supplementary retreatment protocol, none of the root canal walls were completely clean in the apical area. The high-energy Er:YAG laser and XP-Endo Finisher R rotary system can be successfully used in endodontic orthograde retreatment under relevant operating parameters.