This clinical report describes immediate tooth auto-transplantation with an autograft of partially demineralized dentin/cementum matrix (pDDM), based on an orthodontic treatment plan for a 16-year-old male patient with a congenital missing tooth (#45). First, vital teeth (#14, #24) were extracted, and root canal filling (#14) was immediately performed with the support of a fixation device. Simultaneously, the tooth (#24) was crushed in an electric mill for 1 min, and the crushed granules were partially demineralized in 2% HNO3 solution for 20 min as the graft material. Next, the donor tooth was transplanted into the created socket (#45), and stabilized using an enamel bonding agent. The wet pDDM was loaded into the location of the congenital missing tooth, and the flap was repositioned. The bonding agent for stabilization was removed at 28 days, and also small contact points between the transplanted tooth and the upper premolar (#14) were added using photopolymerizable composite resin. X-ray photos were taken sequentially, and there were no postoperative complications. The radiographic images showed that the periodontal ligament space and alveolar ridge line could be observed at 18 months. The pDDM was harmonized with the mandible, and the remodeled bone-like shadow was observed in the graft region. We concluded that immediate tooth transplantation with root canal fillings and autogenous pDDM may be a valuable alternative to dental implanting or bridge formation for patients with a congenital missing tooth, followed by orthodontic treatment.