Luminal A breast cancer is characterized by the expression and activity of estrogen receptor-α (ERα), a biomarker and therapeutic target. While endocrine therapies targeting ER signaling have shown efficacy, long-term success is limited by the development of resistance. Almost 40% of ER-positive breast cancer patients presenting with late-stage disease either fail to respond to endocrine therapies or relapse due to acquired resistance, leading to poor prognosis. Here, we focused on aromatase inhibition, which is administered to patients in menopause, and found strong upregulation of GLYATL1 (glutamine-N-acyltransferase) in two endocrine therapy-resistant in vitro models. Increased expression of GLYATL1 was found also in patients during treatment and its expression was significantly correlated with poor survival in luminal A breast cancer patients after administration of aromatase inhibitors. Interference with GLYATL1 reversed the resistance phenotype in both in vitro models. GLYATL1 expression was associated with overall decreased TCA cycle activity, however, accumulation of succinate, and with altered histone modifications. Unexpectedly, GLYATL1 expression was found to be positively regulated by estrogen-receptor, yet only in estrogen-deprived conditions suggesting that GLYATL1 is a novel factor in endocrine therapy-resistance of luminal breast cancer, impinging on metabolism and epigenetic gene regulation.