Rutin is a common dietary flavonoid with important pharmacological activities. However, its application in the food industry is limited mainly because of its poor water-solubility. The nano-scale ferritin cage provides an ideal space for subtle encapsulation of hydrophobic rutin molecules. This study describes the preparation of novel homogeneous soybean seed ferritin stabilized rutin nanodispersions (FRNs) by a unique reversible dissociation and reassembly of the apoferritin. The characteristics including the water-solubility, morphology, leakage kinetics, and stability of the FRNs were investigated. Results indicated that the rutin molecules could be successfully encapsulated within the protein cages with a rutin/protein molar ratio of 30.1 to 1, and the encapsulation and loading efficiency were 25.1% (w/w) and 3.29% (w/w), respectively. In vitro experiments of rutin release demonstrated that the entrapment of rutin was effective, with more than 75% (w/w) still encapsulated in the ferritin cage after storage for 15 days. Furthermore, the thermal and UV radiation stability of ferritin trapped rutin was greatly improved due to the encapsulation as compared to free rutin. Additionally, the antioxidant activity of FRNs was partly retained as compared to free rutin molecules. This study provides a novel strategy for the design and fabrication of nanocarriers providing water-insoluble molecules with protection and stabilization.