An alloplastic total joint replacement (TJR) is an effective and reliable treatment option in non-salvageable end-stage temporomandibular joint (TMJ) disease. However, unilateral alloplastic TJR of the TMJ (TMJ TJR) could affect the other side natural joint because the physiologic action of both condyles is quite different during mandibular movement. In this study, we examined whether the unilaterally replaced alloplastic TMJ TJR affects the other side natural joint condition over long periods of time. Eight patients who received alloplastic TJR on one side were subjects in this study. All alloplastic TJR implants were stable in situ. The average maximum mouth opening was 37.5 mm (range 19–49 mm) pre-operatively and 44.1 mm (range 34–57 mm) post-operatively. This parameter gradually increased and reached the maximum at about twelve months after surgery. The post-operative change of pain level was significantly reduced from 3.5 to 0 on a pain scale of zero to ten. No significant complications in any joints were observed within the follow-up period. The shape of the natural joint sides showed slight changes but were functionally stable during the observation period. In this study, unilateral alloplastic TJR showed stable and reliable clinical results, either alloplastic TJR or healthy joint sides for quite long period of time.