We report boron nitride nanoflakes (BNNFs), for the first time, as a nanofiller for polymer electrolyte membranes in fuel cells. Utilizing the intrinsic mechanical strength of two-dimensional (2D) BN, addition of BNNFs even at a marginal content (0.3 wt %) significantly improves mechanical stability of the most representative hydrocarbon-type (HC-type) polymer electrolyte membrane, namely sulfonated poly(ether ether ketone) (sPEEK), during substantial water uptake through repeated wet/dry cycles. For facile processing with BNNFs that frequently suffer from poor dispersion in most organic solvents, we non-covalently functionalized BNNFs with 1-pyrenesulfonic acid (PSA). Besides good dispersion, PSA supports efficient proton transport through its sulfonic functional groups. Compared to bare sPEEK, the composite membrane containing BNNF nanofiller exhibited far improved long-term durability originating from enhanced dimensional stability and diminished chronic edge failure. This study suggests that introduction of properly functionalized 2D BNNFs is an effective strategy in making various HC-type membranes sustainable without sacrificing their original adventurous properties in polymer electrolyte membrane fuel cells.