Background: Chronic myeloid leukemia (CML) is a rare disease in children and treated with tyrosine kinase inhibitors (TKI) and with allogeneic hematopoietic stem cell transplantation (HSCT) still in many cases. Case: We describe an 8-year-old patient with CML treated with two different TKIs before proceeding to allogeneic HSCT. Despite successful engraftment, prompt rejection of the graft was followed by autologous reconstitution. TKI therapy was reintroduced post-rejection in anticipation of relapse but shortly discontinued due to low white blood cell and neutrophil counts. The patient has remained disease-free over 5 years after graft rejection and without further therapy. Conclusion: This case suggests that even a short antileukemic effect by an allogeneic transplant may succeed in eradicating CML.