BACKGROUND: The aim of this study was to assess correlation between pain and degenerative bony changes on cone-beam computed tomography (CBCT) images of temporomandibular joints (TMJs). METHODS: Two hundred eighty-three temporomandibular joints with degenerative bony changes were evaluated. Pain intensity (numeric rating scale, NRS) and pain duration in patients with degenerative joint disease (DJD) were also analyzed. We classified condylar bony changes on CBCT into five types: osteophyte (Osp), erosion (Ero), flattening (Fla), subchondral sclerosis (Scl), and pseudocyst (Pse). RESULTS: Degenerative bony changes were the most frequent in the age groups of 10~19, 20–29, and 50~59 years. The most frequent pain intensity was “none” (NRS 0, 34.6%) followed by “annoying” (NRS 3–5, 29.7%). The most frequent condylar bony change was Fla (219 joints, 77.4%) followed by Ero (169 joints, 59.7%). “Ero + Fla” was the most common combination of the bony changes (12.7%). The frequency of erosion was directly proportional to NRS, but the frequency of osteophyte was inversely proportional. The prevalence of Ero increased from onset until 2 years and gradually decreased thereafter. The prevalence of Osp, Ero, and Pse increased with age. CONCLUSIONS: Osp and Ero can be pain-related variables in degenerative joint disease (DJD) patients. “Six months to 2 years” may be a meaningful time point from the active, unstable phase to the stabilized late phase of DJD.