Abstract: Second- and third-generation (2/3G) tyrosine kinase inhibitors (TKIs) possess excellent treatment effects on chronic myeloid leukemia (CML), and at least one 2/3G TKI is mostly incorporated into the first treatment of CML in all phases. However, the impact of 2/3G TKIs on subsequent allogeneic stem cell transplantation (allo-SCT) remains to be elucidated. We retrospectively evaluated how pretransplant therapy with TKIs affects the outcome of allo-SCT for CML using the clinical data of thirty-two patients with CML transplanted between 2001 and 2020 at our institution. Except for 11 patients who remained in the chronic phase (CP) until the time of allo-SCT, 10 patients were initially diagnosed with accelerated or blastic phase (AP/BP), and 11 patients progressed to AP/BP during the treatment for CP. With subsequent use of 2/3G TKI or imatinib (IM), 10 and 4 patients returned to the second CP at the time of allo-SCT, respectively. In univariate analysis, pretransplant use of 2/3 GTKI was significantly associated with higher 5-year overall survival (91.7%) and relapse-free survival (75.0%) than the use of IM (37.5% and 12.5%, respectively) in patients presenting with or progressing to AP/BP before allo-SCT. Our results suggest that pretransplant use of 2/3G TKI improves the outcome of allo-SCT in CML patients who present with AP/BP at diagnosis or progress to the advanced phase thereafter.