Knowledge of the root canal anatomy and its variations is essential for successful completion of the endodontic treatment. Root canal treatment of maxillary second molars with aberrant canal configuration can be challenging. The incidence of two palatal canals in a palatal root is quite rare in maxillary molars. The novel diagnostic aids such as cone-beam computed tomography (CBCT) help in the successful management of such cases. This case report describes the successful diagnosis and treatment of a maxillary second molar with two palatal canals, merging at the apical third of the root.