How to treat CML patients who are resistant to inhibitors of BCR‐ABL tyrosine kinase such as Imatinib is a very important and urgent issue in clinical hematology. Here, we report a case of Imatinib‐treated CML in which intradermally administered WT1 peptide vaccine elicited WT1‐specific immune responses and the resultant reduction in the persistent residual disease in co‐administration of Imatinib. BCR‐ABL mRNA levels were being maintained under the detection limit for 8 months since week 77 of vaccination. No adverse effects except local erythema at the injection sites were observed. The tetramer assay revealed that the decrease in BCR‐ABL mRNA levels was associated with the increase in frequency of WT1‐specific cytotoxic T lymphocytes, notably effector‐memory type of that, in the patient’s peripheral blood. The case presented here indicates that WT1 peptide vaccine may become a safe and cure‐oriented therapy for CML patients who have residual disease regardless of the treatment with Imatinib.