Myeloid blood cancers, including acute myeloid leukaemia, myelodysplasia and myeloproliferative neoplasms, are caused by acquired mutations within haematopoietic stem cells. These mutations lead to increased proliferation and enhanced self renewal. Mutations in epigenetic regulators such as DNMT3A have been associated with adverse prognosis, particularly in certain subtypes of acute myeloid leukaemia. Here, we develop isogenic models of AML, containing Dnmt3a mutations in combination with Npm1c and Flt3ITD mutations. Dnmt3aR878H reprogrammed AML stem cell populations, leading to enhanced self-renewal, quiescence and caused chemotherapy resistance. These pathways are regulated through hypomethylation at stem cell promoters. Dnmt3a mutations induce chemotherapy resistance, correlating with adverse prognosis. We have identified strategies that can overcome this chemotherapy resistance, through cell cycle independent targeting of stem cell populations, or through enforced exit from quiescence.