Background: Primary intraosseous carcinoma (PIOC) is a rare malignant odontogenic tumor that predominantly occurs in males older than 50 years. PIOC can be misdiagnosed as odontogenic cyst because it occasionally shows well-defined border on radiography. In this study, a case of a 14-year-old female with PIOC who was misdiagnosed with odontogenic cyst clinically is reported along with a literature review of pediatric PIOC cases.Case Presentation: A 14-year-old female patient presented with painful swelling on the mandibular right premolar area. There was a radiolucent lesion with a well-defined border in panoramic view. She was diagnosed with odontogenic cyst, and the cystic mass was enucleated with extraction. However, the biopsy result was consistent with PIOC. After cancer work-up, she underwent partial mandibulectomy, selective neck dissection, and reconstruction with a fibular free flap. Although the surgical resection margins were clear, local recurrence and lung metastasis occurred four months after surgery. She underwent concurrent chemo-radiation therapy, but the prognosis was poor.Conclusions: PIOC should be diagnosed differentially from odontogenic cyst even in pediatric populations.