Congenital cholesteatoma is typically an expanding cystic mass of keratinizing squamous epithelium located medial to the intact tympanic membrane in patients with no prior history of perforation, otorrhea and ear. It is generally thought to be a progressive disease and is usually surgically removed upon detection as the first-choice treatment. As such, it is rare to be observed for a long term without progression. Here we report a rare case of congenital cholesteatoma that remained in an undetectable size and did not deteriorate mild hearing loss for 12 years. A seven years old boy was referred to us with right hearing impairment. Pure-tone audiometry found conductive hearing loss with an air-bone gap of 25 dB and a high-resolution computed tomography (CT) scan found the eroded long process of incus but did not detect any soft tissue density indicating congenital cholesteatoma. He initially did not wish to undergo surgery. His hearing level and image finding remained virtually unchanged during the next 12 years of the follow-up period. Twelve years later, endoscopic ear surgery was performed, which revealed a very small cholesteatoma mass, an eroded long process of the incus and ossicular chain discontinuities. We suspect that the cholesteatoma was originally larger, partially eroded the incus, then regressed to a very small size, and remained small for at least 12 years under our observation.