Compound odontoma, a benign epithelial odontogenic tumor, manifests disordered clinical and pathological features due to the formation of a variant tooth-like structure; moreover, it is frequently associated with disrupted permanent tooth eruption, which is a characteristic of supernumerary teeth. Here, we present a rare case of compound odontoma in a 7-year-old male with a unique and an informative clinical course. The patient presented compound odontoma and supernumerary tooth both in the same perifollicular region of the left permanent central incisor of the maxilla; however, each lesion was radiographically detected at different times. Interestingly, an odontoma-like entity appearing as a dense radiopaque lesion was recognized only 1 year and 6 months after extracting the primary incisor and impacted supernumerary teeth, respectively. A secondary lesion subsequently migrated to the impacted crown of the permanent incisor. The surgical specimen revealed partial involvement with a developing odontoma.