The objective of the present study was to evaluate and compare the dentin removal capacity of Endogal Kids and Reciproc Blue NiTi alloy endodontic reciprocating systems for root canal treatments in primary second molar teeth via a micro-computed tomography (micro-CT) scan. Materials and Methods: Sixty root canal systems in fifteen primary second molar teeth were chosen and classified into one of the following study groups: A: EK3 Endogal Kids (n = 30) (EDG) and B. R25 Reciproc Blue (n = 30) (RB). Preoperative and postoperative micro-CT scans were uploaded into image processing software to analyze the changes in the volume of root canal dentin using a mathematical algorithm that enabled progressive differentiation between neighboring pixels after defining and segmenting the root canal systems in both micro-CT scans. Volumetric variations in the root canal system and the root canal third were calculated using a t-test for independent samples or a nonparametric Mann–Whitney–Wilcoxon test. Results: Statistically significant differences (p = 0.0066) in dentin removal capacity were found between the EDG (2.89 ± 1.26 mm3) and RB (1.22 ± 0.58 mm3) study groups for the coronal root canal third; however, no statistically significant differences were found for the middle (p = 0.4864) and apical (p = 0.6276) root canal thirds. Conclusions: Endogal and Reciproc Blue NiTi endodontic reciprocating systems showed similar capacity for the removal of root canal dentin, except for the coronal root canal third, in which the Reciproc Blue NiTi endodontic reciprocating system preserved more root canal dentin tissue.