Acquisition of resistance to gemcitabine in pancreatic cancer remains a major challenge. Here, we investigated the metabolite profiles by liquid chromatography-mass spectrometry between gemcitabine-resistant and parental cancer cells, and found that lactic acid amount and lactate dehydrogenase activity were increased in gemcitabine-resistant cancer cells. We observed the elevated lactate dehydrogenase A (LDHA) expression significantly correlated with recurrent pancreatic cancer patients following gemcitabine treatment and with cancer stem cell (CSC) properties. By approaching the comparative array-based microRNA expression and transcription analysis, we further identified that FOXO3a-induced miR-4259 directly targeted the 3'untranslated region of LDHA and reduced LDHA expression, leading to decreased gemcitabine resistance and CSC phenotypes. Our findings suggest that LDHA might serve as a therapeutic target for pancreatic cancer, particularly gemcitabine-resistant pancreatic cancer, and may provide evidence of an underlying epigenetic regulation of LDHA by FOXO3a/miR-4259, which appears to be involved in cancer stemness and the chemoresistance of pancreatic cancer.