Mitochondrial dysfunction has been considered a critical component in the development of diabetes. In pancreatic β-cells especially, mitochondrial dysfunction impairs insulin secretion and the eventual apoptosis of β-cells. The aim of this study was to elucidate the molecular mechanism underlying these events. Metabolic stress induced by antimycin or oligomycin was used to impair mitochondrial function in MIN6N8 cells, a mouse pancreatic β-cells, and the effects of glucokinase (GCK) and mitochondria were investigated. Concurrent with reduction in mitochondrial membrane potential (ΔΨm) and cellular ATP content, impaired mitochondrial function reduced GCK expression and resulted in decreased insulin secretion and β-cell apoptosis. Specifically, lowered GCK expression led to decreased interactions between GCK and mitochondria, which increased Bax binding to mitochondria and cytochrome C release into cytoplasm. However, these events were blocked by treatment with the antioxidant, N-acetyl-cysteine (NAC), as well as GCK overexpression. Moreover, examination of the GCK promoter in antimycin-treated cells demonstrated that the promoter region within −287 bases from transcription site is involved in the transcriptional repression of GCK by mitochondrial stress, whose region contains a putative binding site for pancreatic duodenal homeobox-1 (PDX-1). Mitochondrial stress reduced PDX-1 expression, and increased ATF3 expression dependent on reactive oxygen species (ROS). Collectively, these data demonstrate that mitochondrial dysfunction by metabolic stress reduces GCK expression through PDX-1 downregulation via production of ROS, which then decreases the association of GCK with mitochondria, resulting in pancreatic β-cell apoptosis and reduction of insulin secretion.