A novel straightforward method is introduced for the non-covalent functionalization of boron nitride nanoflakes (BNNFs) using 1-pyrenemethyl methacrylate (1-PMA) as both nanofiller and crosslinking agent for applications in polymer electrolyte membrane (PEM) fuel cells and PEM water electrolyzers. By leveraging boron nitride’s mechanical strength and gas barrier properties, remarkable improvements are achieved in Young’s modulus (32.1% and 96.6% increases for cBN-EPDM and cBN-PDMS, respectively) and reduced hydrogen permeability (55.7% and 42.7% reductions for cBN-EPDM and cBN-PDMS) with addition of just 0.5 wt% to commercial gasket materials such as EPDM rubber and silicone polymer. Furthermore, the inclusion of 1-PMA enables a high crosslinking density (17.1% and 3.4% increase for cBN-EPDM and cBN-PDMS, respectively), leading to nanocomposites with exceptional chemical durability in both acidic (6.6% and 0.2% loss for cBN-EPDM and cBN-PDMS, respectively) and alkaline (3.8% and 2.1% loss for cBN-EPDM and cBN-PDMS, respectively) environments, as well as enhanced thermal stability. PEMFC, PEMWE, and AEMWE performances are evaluated by comparing with commercial alternatives, demonstrating comparable or superior performance. This study offers a viable strategy for enhancing the performance and durability of materials used in fuel cells and water electrolyzers by optimizing the functionalization of 2D BNNFs and maintaining their inherent properties.