To demonstrate the role of autophagy and incretins on fructose‐induced alteration in β‐cell mass and function. Methods: Normal Wistar rats were fed (3 weeks) with commercial diet without (C) or with 10% fructose in drinking water (F) alone or plus sitagliptin (CS and FS) or exendin‐4 (CE and FE). Serum levels of metabolic/endocrine parameters, β‐cell mass, morphology/ultrastructure and apoptosis, VMP1 expression and glucose‐stimulated insulin secretion (GSIS) were studied. Complementary, islets isolated from normal rats were cultured (3 days) without (C) or with F and F plus exendin‐4 (FE) or chloroquine (FCQ). Expression of autophagy related‐proteins (VMP1 and LC3), apoptotic/antiapoptotic markers (caspase‐3 and Bcl‐2), GSIS and insulin mRNA levels were measured. Results: F rats developed impaired glucose tolerance (IGT) and a significant increase in plasma triglyceride, TBARS, insulin levels, HOMAIR and HOMA‐β indexes. Significant β‐cell mass reduction was associated to an increased apoptotic rate and morphological/ultrastructural changes indicative of autophagic activity. All these changes were prevented by either sitagliptin or exendin‐4. In cultured islets, F significantly enhanced insulin mRNA and GSIS, decreased Bcl‐2 mRNA levels and increased caspase‐3 expression. Chloroquine reduced these changes suggesting autophagy participation in this process. Indeed, F induced the increase of both, VMP1 expression and LC3‐II, suggesting that VMP1‐related autophagy is activated in injured β‐cell. Exendin‐4 prevented islet‐cell damage and autophagy development. Conclusions: VMP1‐related autophagy is a reactive process against Finduced islet dysfunction, being prevented by exendin‐4 treatment. This knowledge could help to use autophagy as potential target for preventing progression from IGT toT2DM.