A 7-year-old boy was diagnosed with RUNX1-RUNX1T1-positive acute myeloid leukemia. Although he achieved complete remission (CR) after conventional chemotherapy, he experienced relapse 6 months after completing initial treatment. The cytoplasm of myeloblasts examined at relapse contained pink giant granules. These myeloperoxidase-positive granules were considered to be pseudo-Chediak-Higashi (PCH) granules. Meanwhile, blasts had acquired genetic alterations such as hypotetraploidy with RUNX1-RUNX1T1 and C-MYC amplification, and a KIT N822K mutation. The patient underwent cord blood transplantation and maintains a second CR. A previous report suggests that C-MYC amplification might be associated with PCH granule formation, and our case supports this hypothesis.