Calcium deposited within a root canal due to exogenous stimuli may hamper root canal treatment. In endodontic treatment, an operating microscope allows the conditions within the root canal to be directly viewed and evaluated. This report describes a case in which an operating microscope was used to facilitate the excision of a calcified structure from within a root canal at an early stage in the treatment of an infection. An 18-year-old man was referred to our clinic due to suspected chronic suppurative apical periodontitis of the right maxillary central incisor. Periapical radiography confirmed the presence of a radioopaque structure inside the root canal that was likely to pose an obstacle to endodontic treatment. After opening the pulp chamber, an operating microscope was used to directly confirm the presence of the calcified structure in the root canal, which was removed using an ultrasonic tip. The infected root canal was treated using calcium hydroxide. Two months later, closure of the apical foramen as a result of calcification of the apical foramen was confirmed and the root canal filled. Using an operating microscope to directly view a structure posing an obstacle to root canal treatment made it possible to perform an excision while avoiding risks such as canal perforation.