In this work, novel proton-exchange membranes (PEMs) based on sulfonated poly(ether ether ketone) (SPEEK) and two-dimensional (2D) sulfonated niobium disulphide (S-NbS2) nanoflakes are synthesized by a solution-casting method and used in vanadium redox flow batteries (VRFBs). The NbS2 nanoflakes are produced by liquid-phase exfoliation of their bulk counterpart and chemically functionalized with terminal sulfonate groups to improve dimensional and chemical stabilities, proton conductivity (σ) and fuel barrier properties of the as-produced membranes. The addition of S-NbS2 nanoflakes to SPEEK decreases the vanadium ion permeability from 5.42 × 10-7 to 2.34 × 10-7 cm2 min-1. Meanwhile, it increases the membrane σ and selectivity up to 94.35 mS cm-2 and 40.32 × 104 S min cm-3, respectively. The cell assembled with the optimized membrane incorporating 2.5 wt% of S-NbS2 nanoflakes (SPEEK:2.5% S-NbS2) exhibits high efficiency metrics, i.e., coulombic efficiency between 98.7 and 99.0%, voltage efficiency between 90.2 and 73.2% and energy efficiency between 89.3 and 72.8% within the current density range of 100-300 mA cm-2, delivering a maximum power density of 0.83 W cm-2 at a current density of 870 mA cm-2. The SPEEK:2.5% S-NbS2 membrane-based VRFBs show a stable behavior over 200 cycles at 200 mA cm-2. This study opens up an effective avenue for the production of advanced SPEEK-based membranes for VRFBs.