Nevus comedonicus is a type of hamartoma that arises from a developmental anomaly of the mesodermal part of the pilosebaceous gland. In most cases of nevus comedonicus, an acne-like skin condition develops. Repeated inflammation can cause a morphological change to the cyst, papule, to abscess. We experienced a case of congenital nevus comedonicus, which led to the formation of large multiple cysts. A 50-year-old man was referred with a $12.5{ imes}10cm$ lobulated mass on the posterior neck and upper back. The patient had a widespread presence of nevus comedonicus in the region ranging from the right superior chest to the posterior neck. The patient had a 30-year history of six prior excisions. A magnetic resonance imaging review led to a diagnosis of nevus comedonicus. Surgical treatment consisted of excision of the mass and wide excision for the patch type of nevus comedonicus around the neck. On histopathology, multiple masses were diagnosed as typical cysts containing keratinized tissue. The diffuse comedone lesions were diagnosed as nevus comedonicus. This case shows that large, multiple cysts can occur as a long-term complication of nevus comedonicus, and also highlights the importance of radical resection to prevent its further invagination.