We report two pediatric cases diagnosed with subcutaneous panniculitis-like T-cell lymphoma (SPTCL) and hydroa vacciniforme-like lymphoma. Both cases were associated with Epstein-Barr virus (EBV) positivity and mutations in the nuclear protein ataxia-telangiectasia (NPAT) gene. These factors complicated the diagnosis, as both patients were initially misdiagnosed and treated for incorrect conditions without clinical improvement. Furthermore, the patients were evaluated by multiple medical specialties before being appropriately referred to dermatology and oncology for further investigation. These rare lymphomas typically present with gradually progressive skin lesions accompanied by fever, pain, or pruritus. Recent studies suggest a link between EBV infection and these types of lymphomas. The NPAT gene plays a crucial role in regulating cell division, and mutations in this gene are believed to contribute to the pathogenesis of both SPTCL and hydroa vacciniforme-like T-cell lymphoma. However, the interaction between EBV infection and NPAT mutations remains poorly understood, further complicating diagnosis and treatment. This diagnostic uncertainty contributed to the complexity of clinical management and ultimately resulted in a poor prognosis, including a fatal outcome in one of the patients.