The study aimed to compare the dynamic thiol/disulfide homeostasis between patients with premature ovarian failure (POF) and healthy women. A total of 77 women, 40 POF and 37 healthy controls, were recruited from a university hospital between December 2013 and June 2015. Blood samples were taken from patients to evaluate follicle stimulating hormone (FSH), luteinizing hormone, estradiol and thiol/disulfide levels. A new, fully automated method was used to measure plasma thiol, total thiol and disulfide levels. Disulfide levels, disulfide/native thiol and disulfide/total thiol ratios were significantly increased, native thiol/total thiol levels were significantly decreased in POF patients compared to controls (p < 0.001). FSH was negatively correlated with native thiol and native thiol/total thiol levels and positively with disulfide, disulfide/native thiol, and disulfide/total thiol levels. This is the first study demonstrating the thiol/disulfide homeostasis in women with POF and may help us understanding the pathophysiology.