Partial edentulism, characterized by the congenital absence of six or more permanent teeth (oligodontia), excluding the third molars, manifests with variable maxillofacial skeletal morphologies and occlusions, depending on the site and number of missing teeth, complicating treatment planning for occlusion and gain of function. Herein, we describe the case of a patient with seven non-syndromic congenitally missing permanent teeth (four in the maxillary and three in the mandibular dentition, excluding the third molars), who underwent orthodontic treatment, restorative procedures, and long-term follow-up for six years. The patient was an 18-year-old man presenting with a chief complaint of congenital absence of some permanent teeth and dental malalignment on the first visit. The mandibular right central incisor, bilateral mandibular second premolars, bilateral maxillary lateral incisors, and bilateral maxillary canines were congenitally absent, while the deciduous maxillary lateral incisors, maxillary canines, and mandibular second molars were over-retained bilaterally. Since the persisting deciduous teeth were remarkably well preserved, the patient was willing to retain them as far as possible; thus, we chose orthodontic and restorative treatment to preserve the deciduous teeth. Occlusion was established after the initiation of dynamic orthodontic treatment; restorative treatment with resin-based materials was performed for the bilateral maxillary deciduous incisors, bilateral maxillary deciduous canines, and bilateral mandibular second primary molars after bracket removal, and the retention phase of orthodontic treatment was initiated. At present, six years after establishing retention, the patient exhibits a good occlusal relationship. It is difficult to achieve complete space closure using orthodontic treatment alone in cases with six or more congenitally missing permanent teeth. In addition to considerations for age, esthetic issues due to missing permanent teeth, and maxillofacial skeletal morphology, it is necessary to preserve the deciduous teeth as much as possible and ensure multidisciplinary medical cooperation, including the transition to prosthodontic treatment during long-term follow-up.