Non-Langerhans cell histiocytosis (non-LCH) is a group of diseases characterized by the proliferation of histiocytes in tissues that is excluded from the diagnostic criteria for LCH. Juvenile xanthogranuloma (JXG) and benign cephalic histiocytosis (BCH) are the most common types of cutaneous non-LCH. These two diseases share similarities in both clinical and histological features, therefore, they can be difficult to differentiate. Thorough physical, dermoscopic, and histopathological examinations are required to distinguish between JXG and BCH. We hereby present two rare cases of non-LCH in pediatric patients, presented with JXG and BCH. The dermoscopic examination of both cases showed a setting-sun appearance, while the histopathological examination revealed Touton giant cells in the JXG case, and massive lymphocyte infiltration in the BCH case. Both patients were treated with 1% topical rapamycin in a split-side comparison for the first 12 weeks, followed by applications on both sides for a total duration of 24 weeks. As a result, there was a significant reduction in the size of the lesion, leading to patient's satisfaction. Rapamycin is an immunosuppressive agent with antineoplastic activity. Rapamycin can be used as an alternative non-invasive topical treatment option for JXG and BCH. However, long-term observations are required to assess its effectiveness and side effects.