Carbon nanofibers functionalized with aminobenzoyl groups (CNF–aminobenzoyl) were prepared via direct Friedel–Crafts acylation in polyphosphoric acid. The functionalization of CNFs was characterized using XPS, FTIR, TGA, and Raman analyses. Hexafluoroisopropylidene-containing polybenzimidazole (6FPBI) composite membranes containing pristine CNFs or CNF–aminobenzoyl were prepared using solvent-assisted dispersion and solvent-casting methods. In this work, the influence of the incorporation of functionalized CNFs on several physicochemical properties of the 6FPBI nanocomposite membranes, including their thermal stability, mechanical strength, and acid doping level, was studied. The results showed that CNF–aminobenzoyl provided better mechanical reinforcement for the nanocomposite membrane, compared to pristine CNF. The SEM observation confirmed the good compatibility between the CNF–aminobenzoyl fillers and the 6FPBI matrix. For the 0.3 wt% CNF–aminobenzoyl/6FPBI composite membrane, the tensile stress was increased by 12% to be 78.9 MPa (as compared to the 6FPBI membrane), the acid doping level was improved to 12.0, and the proton conductivity at 160 °C was measured above 0.2 S cm⁻¹. Furthermore, the fuel cell performance of the membrane electrolyte assembly (MEA) for each nanocomposite membrane was evaluated. The maximum power density at 160 °C was found up to 461 mW cm⁻² for the MEA based on the 0.3 wt% CNF–aminobenzoyl/6FPBI composite membrane.