Hypophosphatemia rickets is a rare disease that is divided into two categories, namely, hereditary and acquirability. Its clinical manifestations include growth disorders, limb deformities and dysfunction, poor mineralization of the teeth, and growth retardation in children as well as hyperparathyroidism, osteoarthritis, osteomalacia, and pseudofracture in adults. Oral manifestations include non-carious teeth with recurrent apical periodontitis, periapical abscess and even cellulitis, periodontitis, and early tooth loss. X-linked hypophosphatemia rickets (XLHR) accounts for approximately 80% of all hypophosphatemia rickets. We report a 3-year-old child with XLHR whose first diagnosis was apical periodontitis of multiple non-carious and non-traumatic teeth. Through medical history, clinical examination, laboratory examination, radiographic findings, genotype testing, and literature analysis, we analyze the pathogenesis, clinical manifestations, radiographic features, diagnosis and differential diagnosis, treatment, and follow-up. This work provides reference for clinical diagnosis and treatment and reduces missed diagnosis and misdiagnosis by dentists.