<p>This study aimed to compare the efficacy of different irrigation activation methods in removing hydrogel from internal root resorption (IRR) cavities and lateral canals created in three-dimensional (3D) printed resin teeth. A total of 100 3D-printed maxillary central incisor teeth incorporating both an IRR cavity and a lateral canal were produced, and a biofilm-mimicking hydrogel was injected into the root canals. The specimens were divided into five groups according to the irrigation activation method used (n = 20): conventional needle irrigation (CNI), EDDY, passive ultrasonic irrigation (PUI), SWEEPS, and XP-Endo Finisher R (XPFR). Each irrigation activation protocol consisted of three repetitions of 20-s activation, using 5&#xa0;mL of distilled water as the irrigant. The amount of remaining hydrogel was evaluated by scoring digital images obtained under a dental operating microscope. Data were analyzed using the Kruskal–Wallis test for multiple group comparisons, Dunn’s post-hoc test with Bonferroni correction for pairwise comparisons, and the Wilcoxon test for comparisons between the two regions (<i>p</i> = 0.05). A significant difference was observed among the irrigation activation methods in terms of hydrogel removal from both the IRR and lateral canal (<i>p</i> &lt; 0.001). Pairwise comparisons revealed that the PUI group achieved significantly superior hydrogel removal compared to all other activation groups (<i>p</i> &lt; 0.05). According to Wilcoxon sign-rank test significantly more hydrogel was removed from the IRR cavity compared to the lateral canal only in SWEEPS group (<i>p</i> = 0.046). PUI was the most effective method for hydrogel removal in both regions. SWEEPS removed more hydrogel from the IRR cavity than from the lateral canal. Within the limitations of this laboratory setup, these findings suggest that clinicians may consider incorporating PUI into their irrigation protocols to enhance debris and biofilm removal in complex root canal anatomies.</p>