Introduction: Pediatric intraosseous lipoma (IOL) is an exceedingly rare, benign tumor, with fewer than 50 cases reported in the literature. No standardized diagnostic or treatment guidelines exist for this condition. Case Presentation: We report the case of a 4-year-old female with a complex fronto-temporal bone IOL, encompassing nearly the entire surface of the hemicranium. She was initially managed with serial imaging and close observation for 30 months before undergoing evaluation from a Multi-Disciplinary Complex Craniofacial Clinic. Due to the significant deformity and craniofacial difference associated with the mass, recommended treatment included resection of the cranial portion of the IOL followed by reconstruction using a porous polyethylene alloplast (Medpor) implant. At 2 years and 8months after the operation, the surgical site was well-healed with interval correction of the craniofacial deformity. Conclusion: This study proposes a structured diagnostic approach for patients presenting with an acquired craniofacial skeletal mass. Treatment for pediatric craniofacial IOL includes multidisciplinary team management, virtual surgical planning with consideration for both correct sequencing and timing of cranial and facial resections, and careful consideration of potential reconstructive cranioplasty modalities.