We present a 1-year-old boy who developed a cutaneous lesion on the trunk and hepatosplenomegaly. Laboratory examination showed leukocytosis with peripheral blasts, atypical monocytosis, anemia, hyper IgG, and a mild elevation of C-reactive protein. Clinical features and skin biopsy findings matched the diagnostic criteria of both juvenile myelomonocytic leukemia (JMML) and Langerhans cell histiocytosis (LCH). Histopathology revealed atypical mononuclear cells that had infiltrated around vessels throughout the dermis in a skin biopsy specimen. These cells were CD1a (+), S-100 (+), CD68 (+), CD207 (-), lysozyme (+), and myeloperoxidase (-). The diagnosis of JMML was confirmed by detection of spontaneous colony formation and granulocyte-macrophage colony-stimulating factor hypersensitivity in vitro, and a somatic NRAS point mutation. Transplantation of bone marrow from an HLA-matched unrelated donor was performed, and the marrow was successfully engrafted. The cutaneous lesion and hepatosplenomegaly were improved at the time of discharge. It is often difficult to distinguish between JMML and LCH-like infiltrates by assessing clinical and light microscopic features of various cutaneous lesions. In the current case, molecular biological analysis enabled us to develop a precise diagnosis.