The link between increased fructose intake and induction of gut and liver dysfunction has been established, while it remains to be understood whether this damage is reversible, particularly in the young population, in which the intake of fructose has reached dramatic levels. To this end, young (30 days old) rats were fed a fructose-rich or control diet for 3 weeks to highlight the early response of the gut and liver to increased fructose intake. After this period, fructose-fed rats were returned to a control diet for 3 weeks and compared to the rats that received the control diet for the entire period to identify whether fructose-induced changes in the gut-liver axis persist or not after switching back to a control diet. Glucose transporter 5 and the tight junction protein occludin were assessed in the ileum and colon. Markers of inflammation and redox homeostasis as well as fructose and uric acid levels were also evaluated in the ileum, colon and liver. From the whole data, it is seen that metabolic derangement elicited by a fructose-rich diet, even after a brief period of intake, is fully reversed in the liver by a period of fructose withdrawal, while the alterations persist in the gut, especially in the ileum. In conclusion, given the increasing consumption of fructose-rich foods in young populations, the present results highlight the risk arising from gut persistent alterations even after the end of a fructose-rich diet. Therefore, dietary recommendations of reducing the intake of this simple sugar is mandatory to avoid not only the related metabolic alterations but also the persistence of these detrimental changes.