A high-performance composite membrane for vanadium redox flow battery (VRB) consisting of ZrO2 nanotubes (ZrNT) and perfluorosulfonic acid (Nafion) was fabricated. The VRB operated with a composite (Nafion-ZrNT) membrane showed the improved ion-selectivity (ratio of proton conductivity to permeability), low self-discharge rate, high discharge capacity and high energy efficiency in comparison with a pristine commercial Nafion-117 membrane. The incorporation of zirconium oxide nanotubes in the Nafion matrix exhibits high proton conductivity (95.2 mS cm−1) and high oxidative stability (99.9%). The Nafion-ZrNT composite membrane exhibited low vanadium ion permeability (3.2 × 10−9 cm2 min−1) and superior ion selectivity (2.95 × 107 S min cm−3). The VRB constructed with a Nafion-ZrNT composite membrane has lower self-discharge rate maintaining an open-circuit voltage of 1.3 V for 330 h relative to a pristine Nafion membrane (29 h). The discharge capacity of Nafion-ZrNT membrane (987 mAh) was 3.5-times higher than Nafion-117 membrane (280 mAh) after 100 charge-discharge cycles. These superior properties resulted in higher coulombic and voltage efficiencies with Nafion-ZrNT membranes compared to VRB with Nafion-117 membrane at a 40 mA cm−2 current density.