Background To evaluate the retreatability of curved root canals obturated with gutta-percha (GP) and iRoot SP using three different Ni-Ti systems through micro-computed tomographic (micro-CT) analysis. Methods A total of 51 curved root canals of permanent molars with angles of curvature ranging from 20° to 40° were used. The root canals were prepared with the ProTaper Next (PTN) rotary system to size 25, .06 taper and filled with iRoot SP and GP using the single cone technique. Samples were randomly divided into three groups (n = 17 each) according to the retreatment system used: Group I. ProTaper Universal Retreatment (PTR) system + ProTaper Next system up to PTN X2; Group II. Waveone Gold (WOG) system (WOG25); Group III. Reciproc Blue (RB) system (RB25). The ability to regain apical patency, the volume of residual filling material, and dentinal microcrack were assessed using micro-CT imaging. Data were analyzed statistically using two-way analysis of variance and chi-square test with a significance level of 5%. Results There were no significant differences among the systems tested in the reestablishment of apical patency and reduction of filling materials (P > 0.05), but RB system exhibited better reestablishment root canal ability in the upper portion of curvature and the reduction of filling materials in the apical third (P < 0.05). Intergroup analysis indicated that PTR system induced significantly more dentinal microcracks than other two systems (P < 0.05). Conclusions All three tested Ni-Ti instruments showed the similar retreatability of curved root canals obturated with gutta-percha and iRoot SP. RB system may be more effective and safer in curved root canal retreatment.