Members of the KDM5 histone H3 lysine 4 demethylase family are associated with therapeutic resistance, including endocrine resistance in breast cancer, but the underlying mechanism is poorly defined. Here we show that genetic deletion of KDM5A/B or inhibition of KDM5 activity increases sensitivity to anti-estrogens by modulating estrogen receptor (ER) signaling and by decreasing cellular transcriptomic heterogeneity. Higher KDM5B expression levels are associated with higher transcriptomic heterogeneity and poor prognosis in ER+ breast tumors. Single-cell RNA sequencing, cellular barcoding, and mathematical modeling demonstrate that endocrine resistance is due to selection for pre-existing genetically distinct cells, while KDM5 inhibitor resistance is acquired. Our findings highlight the importance of cellular phenotypic heterogeneity in therapeutic resistance and identify KDM5A/B as key regulators of this process. Display omitted •KDM5 activity modulates response and resistance to endocrine therapies•Endocrine resistance is due to selection for pre-existing distinct cell populations•Acquired KDM5 inhibitor resistance is epigenetic, including gain of ER signaling•Transcriptomic but not genetic heterogeneity is associated with higher KDM5B Hinohara et al. demonstrate that histone demethylases KDM5A and KDM5B are key regulators of phenotypic heterogeneity in estrogen receptor (ER)-positive breast cancer. Inhibition of KDM5 activity increases sensitivity to endocrine therapy by modulating ER signaling.