Background <p>Internal root resorption is an infrequent resorption of dentin and stands among one of the endodontic challenges which comprises two types: internal replacement and inflammatory resorption. Regardless of the location, root resorption does not regress and continues to cause discomfort or sometimes tooth loss if left untreated. Internal replacement resorption is rarer compared with the other type of internal resorption. Regarding the scarcity of internal replacement resorption, the present article reports a case of endodontic management of internal replacement resorption by using NeoPutty mineral trioxide aggregate and cone-beam computed tomography to illustrate and clarify characteristics, diagnosis, possible etiologies, and treatment modalities for internal replacement resorption.</p> Case presentation <p>A 55-year-old Iranian man was referred for a sinus tract. Periapical radiographs revealed a periradicular lesion and cone-beam computed tomography showed the internal replacement resorption of teeth nos. 8 and 9. The root canal was explored using ultrasonic tips under magnification. Irrigation was done using 2.5% sodium hypochlorite with ultrasonic irrigation. Calcium hydroxide was placed in the root canal for 2&#xa0;weeks as an intracanal medicament. At the next appointment, after calcium hydroxide removal, the root canal was dried and obturated using NeoPutty mineral trioxide aggregate. At the 2&#xa0;year follow-up, the teeth were unresponsive to percussion test.</p> Conclusion <p>Traumatic injuries may lead to internal replacement resorption, which has a progressive nature and urges instant endodontic management. Mineral trioxide aggregate seems to be a promising material for internal replacement resorption. Besides, cone-beam computed tomography and dental operative microscopes can improve the outcome of endodontic therapy in certain challenging cases.</p>