A hybrid membrane of Nafion/amino-silica (amino-SiO2) for vanadium redox flow battery (VRB) systems is prepared via the sol–gel method to improve the selectivity of the Nafion membrane, to reduce the crossover of vanadium ions, and to decrease water transfer across the membranes. The sulfonated pores of the pristine Nafion membrane are filled with amino-SiO2 nanoparticles localized by electrostatic interaction. The permeability of vanadium ions through the Nafion/amino-SiO2 hybrid membrane is determined by electrometric titration. The results indicate the crossover of vanadium ions through the hybrid membrane is 26.8% of the pristine Nafion membrane. The presence of amino-SiO2 in the hybrid membrane is verified by X-ray photoelectron spectroscopy (XPS). Nafion/amino-SiO2 hybrid membrane exhibits through plane conductivity about the same as the pristine Nafion membrane. The ion exchange capacity (IEC) of the hybrid membrane is 9.4% higher than that of the pristine Nafion membrane. In addition, Nafion/amino-SiO2 hybrid membrane exhibits a higher coulombic efficiency (CE), voltage efficiency (VE), and energy efficiency (EE) over a range of current densities from 20 to 80 mA cm−2. The performance of VRB with Nafion/amino-SiO2 hybrid membrane varies little around a charge–discharge current density of 80 mA cm−2 for 150 cycles. Thus, the Nafion/amino-SiO2 hybrid membrane can suppress the vanadium ions crossover in VRB.