Fuel cells offer a promising route to eliminating in-flight emissions from regional aviation, but certification requires proof that stacks can withstand the vibration and shock environment of turboprop aircraft. As part of the EU-funded NEWBORN project, we combined detailed finite element modeling with shaker tests to evaluate the vibration immunity of PowerCell Group’s prototype stack. The numerical model combined an orthotropic, two-zone 3D mesh of the cell package with reduced-order representations of plates, compression bands, disc springs and the mounting cage. The assembled stack was excited between 10 and 300 Hz using pseudo-random and sine-sweep inputs up to 2.0 g, from which 54 frequency response functions were obtained. The tuned model accurately reproduced the first global modes and captured the overall dynamic behavior with good, though not perfect, agreement. The combined numerical–experimental methodology therefore offers a framework for refining test campaigns and delivering early, qualitative evidence of vibration immunity in fuel cell stacks destined for flight.