Detailed case reports of autologous recovery of hematopoiesis after hematopoietic stem cell transplantation with myeloablative conditioning (MAC) are scarce. We present a rare case of a 3-year-old male with relapsed KMT2A-rearranged acute lymphoblastic leukemia (ALL) who experienced autologous recovery following secondary engraftment failure after cord blood transplantation (CBT) with MAC. Similar to previous reports, we detected unusual chromosomal abnormalities, which differed at each bone marrow examination. He remains alive without relapse of ALL 12 months after CBT. As the rate of recurrence or late occurrence of secondary malignant neoplasm remains unclear, careful follow-up is required, especially in pediatric patients.