Here, we report the management of a type I endoperiodontal lesion with furcation bone loss. A 59-year-old female attended our hospital with the chief complaint of mobility of tooth 46 and recurrent gingival swelling around the tooth. She previously received dental treatment from two dentists, but her condition did not improve. The tooth manifested the symptoms of typical periodontitis, such as gingival swelling, tooth mobility, pus discharge from the periodontal pocket and furcation bone loss. The tooth had no caries and the pulp reacted to an electric pulp test. Careful examination of the gingiva revealed traces of dental fistula. X-ray examination via a gutta percha inserted into the fistula revealed that furcation bone loss was associated with the periapical lesion. We diagnosed a type I endoperiodontal lesion, and applied Periocheck, a detection kit for peptidase-producing bacteria, to check for decreases in bacteria in the furcation and root canals. Soon after non-surgical root canal treatment, the condition of tooth 46 improved without periodontal treatment. After confirming a negative score with Periocheck, the root canal was filled. After 3 months, the furcation bone loss was on the way to recovery. These results indicate that proper diagnosis and confirmation of a decrease in root canal bacteria are important for treating endoperiodontal lesions.