Aim: To compare and evaluate the removal of CeraSeal, Bioceramic Sealer, and AH Plus for retreatment using two rotary retreatment systems—R-Endo and GPR files. Materials and methods: Depending on the sealer used for obturation, a total of 54 extracted mandibular permanent premolars were instrumented with ProTaper files up to F3. Samples were divided into three groups (n = 18 each): group I—CeraSeal group; group II—Bioceramic (Prashanti) group; group III—AH Plus group. The samples were then subjected to cone beam computed tomography (CBCT) imaging to calculate the volume of the filled material. The specimens in each group were then further divided into two subgroups (n = 9 each) based on the retreatment file system employed: (A) R-Endo files, (B) GPR files. All the samples were evaluated for remnants of filling material by CBCT imaging. The results were analyzed using one-way analysis of variance (ANOVA), followed by a post hoc Tukey test. Results: When comparing the sealers’ retrievability, R-Endo demonstrated superior removal efficiency in all sealers, with a statistically significant difference. Group IIA showed the highest removal efficiency (96.35%), whereas group IIIB showed the lowest removal efficiency (67.80%). Conclusion: CeraSeal and Bioceramic Sealer were removed more easily compared to AH Plus Sealer. When comparing the retreatment file system, R-Endo showed better removal efficiency than Mani GPR. Clinical significance: The retrievability of Bioceramic Sealer can be difficult since it bonds with dentin via a mineral infiltration zone. This can present a potential challenge during retreatment procedures. Additionally, understanding the efficiency of R-Endo and the GPR file system in removing obturating material is essential for clinicians to effectively choose and respond to such challenging scenarios when encountered.