Hypophosphatasia (HPP) is a rare genetic disorder; affected patients may experience early exfoliation of primary teeth, especially anterior teeth. However, there have been few reports regarding longitudinal follow-up for primary teeth, especially posterior teeth, until their replacement with permanent teeth. Here, we describe a patient with HPP who underwent follow-up from 1 to 9 years of age. A 14-month-old boy was referred to our hospital with the chief complaint of early loss of primary anterior teeth. He was diagnosed with odonto-type HPP by his pediatrician, due to low serum alkaline phosphatase concentration and early exfoliation of primary teeth with bone hypomineralization. The patient experienced exfoliation of three additional primary anterior teeth by 4 years and 1 month of age. Partial dentures were applied for space maintenance; there were no problems regarding subsequent replacement with permanent teeth in the anterior region. However, the primary mandibular right first molar appeared to be submerged when the patient was 8 years and 3 months of age; the severity of submergence was greater when the patient was 9 years of age. The affected primary molar was considered to be ankylosed; it was extracted when the patient was 9 years and 4 months of age. Histopathological analysis of the tooth revealed disturbed cementum formation, which is a typical characteristic of teeth in patients with HPP. On the basis of these findings, we hypothesize that the disturbed cementum formation could lead to susceptibility to early exfoliation of anterior teeth, as well as occurrence of ankylosis involving posterior teeth.