Oxidative stress is one of the key factors that contributes to the pathogenesis of keratoconus (KC). Macroautophagy is a vital cellular mechanism that is activated in response to oxidative stress. The aim of this study was to understand the role of the autophagic lysosomal pathway in the oxidative damage of KC corneal epithelium and the human corneal epithelial cell line (HCE).The corneal epithelium was collected from 78 KC patients undergoing corneal cross-linking or topography guided photorefractive keratectomy. We performed microarray, qPCR and western blot analysis for the expression of autophagy markers on this epithelium from patients with different clinical grades of KC. A differential expression pattern of autophagy related markers was observed in the diseased corneal cone-specific epithelium compared to matched peripheral epithelium from KC patients with increasing clinical severity. Human corneal epithelial cells exposed to oxidative stress were analyzed for the expression of key proteins associated with KC pathogenesis and the autophagic pathway. Oxidative stress led to an increase in reactive oxygen species and an imbalanced expression of autophagy markers in the HCE cells. Further, reduced levels of Akt/p70S6 Kinase, which is a known target of the mTOR pathway was observed in HCE cells under oxidative stress as well as in KC epithelium. Our results suggest that an altered expression of proteins suggestive of defective autophagy and is a consequence of oxidative damage. This could play a possible role in the pathogenesis of KC.