Allogeneic hematopoietic cell transplantation (allo-HCT) remains a key treatment for patients with chronic myeloid leukemia (CML) in blast phase (CML-BP) or tyrosine kinase inhibitor (TKI)-resistant chronic phase (CML-CP). We retrospectively analyzed 75 patients who underwent allo-HCT at four U.S. centers from 2005 to 2023. Of these, 60 had CML-BP (26 myeloid, 34 lymphoid) and 15 had TKI-resistant CML-CP. Median overall survival (OS) was 50 months in myeloid blast phase (MBP) and not reached in lymphoid blast phase (LBP) or CML-CP. MBP had higher relapse rates and inferior leukemia-free survival (LFS) compared to LBP and CML-CP. Outcomes were worse in transformed MBP versus de novo MBP, and in those with 7/7q- deletions. Post-HCT TKI maintenance did not significantly affect relapse or survival. Our findings support allo-HCT as an effective treatment option in CML-BP and TKI-resistant CML-CP, with outcomes influenced by disease biology and cytogenetic features at transformation.