Herein, we report a patient with polycythemia vera (PV) who exhibited Philadelphia chromosome (Ph) positive CML-like clinical features after 13 years of hydroxycarbamide administration and successful treatment with a tyrosine kinase inhibitor (TKI). She was 64 years old when initially diagnosed with PV and was confirmed to be negative for BCR-ABL translocation. Thirteen years later, with increasing white blood cell and platelet counts, a BCR-ABL positive clone emerged and the JAK2V617F mutation disappeared. After TKI treatment, the BCR-ABL copy number decreased and the JAK2V617F mutation was again detected. Furthermore, MPN clinical features were observed. This case provides insights into the clonal divergence and growth advantage of the Ph positive clone over the MPN clone. Whether JAK2V617F is an MPN initiating event or a secondary mutation has been a point of discussion for the past several years. This issue is also considered in the present report.