Tartary buckwheat (Fagopyrum esculentum) is widely used in the food industry due to its functionality, which is related to its high rutin content. However, rutin is easily converted into quercetin by an endogenous enzyme during processing, resulting in a bitter taste. In this study, rutin-enriched Tartary buckwheat flour extracts (TBFEs) were obtained by hydrothermal treatments (autoclaving, boiling, and steaming), and their antioxidant activity was evaluated in human intestinal cells. The intestinal absorption of the hydrothermally treated TBFEs was also investigated using in vitro models of intestinal barriers and an ex vivo model of intestinal absorption. The results demonstrated that all of the hydrothermally treated TBFEs had increased rutin, total polyphenol, and total flavonoid contents, which enhance the in vitro and intracellular radical scavenging activities. Antioxidant enzyme activity, cellular uptake efficiency, in vitro intestinal transport efficacy, and ex vivo intestinal absorption of the hydrothermally treated TBFEs were also enhanced compared with those of native TBFE or standard rutin. These findings suggest the promising potential of hydrothermally treated TBFEs for a wide range of applications in the functional food industry.