Root canal treatment is a routine endodontic procedure, but complications such as root perforations can compromise prognosis. Perforations create communication between the root canal system and supporting tissues, leading to bacterial contamination, periodontal involvement, and potential tooth loss if untreated. This case report highlights the management of a furcal perforation in a maxillary first molar using Biostructure Mineral Trioxide Aggregate (MTA) putty, with a review of literature on perforation classification, diagnosis, prevention, and treatment strategies. A 14-year-old male presented with pain and incomplete root canal treatment in relation to tooth 16. Clinical and radiographic examination revealed furcal perforation and incomplete obturation. The canals were cleaned and shaped, and the perforation was sealed with Biostructure MTA putty. Subsequent obturation was performed with gutta-percha and BioACTIVE RCS, followed by composite restoration and zirconia crown placement. Follow-up at 3, 6, and 12 months demonstrated successful healing, bone regeneration in the furcal area, and absence of symptoms. Successful management of perforations depends on early diagnosis, appropriate material selection, and operator expertise. MTA has proven effective due to its biocompatibility, sealing ability, and regenerative potential. Literature supports its long-term success in perforation repair, with favorable outcomes in both clinical and radiographic evaluations. Furcal perforations, if managed promptly with suitable materials such as MTA, can achieve predictable healing and favorable prognosis. This case reinforces MTA’s role as a gold standard in perforation repair and highlights the importance of careful diagnosis and treatment planning in endodontics.