Mastocytosis arises from the abnormal growth and accumulation of mast cells within the body’s organ systems. Within the pediatric age group, systemic mastocytosis is exceptionally rare, with only a few reported cases in the medical literature. Here, we report a case detailing a solitary skull lesion in a 10-year-old child as the sole identified manifestation of systemic mastocytosis. She presented with neurologic symptoms without any allergic or systemic manifestation. The child was initially diagnosed with hemangiopericytoma, with the differential diagnosis of atypical meningioma. The patient underwent surgery and histopathological examination confirmed the diagnosis of systemic mastocytosis. Unfortunately, the patient presented with recurrence, necessitating another surgery that again confirmed the diagnosis. Multidisciplinary team collaboration integrating clinical, radiographic, and immunophenotypic correlations is vital in the diagnosis and management of this sporadic condition.