Anatomic variations can significantly contribute to the incidence of endodontic mishaps. Perforations and separated instruments form the bulk of such mishaps. Furcal perforations are undesired complications of endodontic treatment, which result in the loss of integrity of the root and further destruction of the adjacent periodontal tissues. Mineral trioxide aggregate (MTA) is a promising material that has been successfully used to repair perforations. This clinical case demonstrates the use of MTA as a repair material for furcal perforation due to an iatrogenic error in radix entomolaris in the mandibular first molar. It also describes the application of ultrasonic technique in the retrieval of separated instrument from the same. Both clinical and radiographic follow-up showed a stable condition without any probing defect, ongoing root resorption, or furcal pathosis.