Genetic changes in juvenile myelomonocytic leukemia (JMML) determine distinct subtypes, treatments and outcomes. JMML with germline CBL mutation and somatic NRAS mutation possibly achieves spontaneous remission, but hematopoietic stem cell transplantation is indicated for other subtypes of JMML. We hereby report a child with JMML harboring a germline CBL mutation (c.1111T>C) and an NF1 variant (c.3352A>G) concurrently. After evaluation, we considered the NF1 variant not the major contributor. After one year of observation, this case had no signs of disease progression. This case highlights the importance of combining available evidence and clinical findings in caring patients with unusual genomic variations.