As in commercial aviation, military aircraft typically use gas turbine engines for propulsion. Regardless of the actual output being thrust or shaft power, each type employs similar working process to produce high energy gasses. Although they are more tolerant to different fuel grades, traditionally jet fuel has been utilized in the past decades. In the recent years, due to emerging problems affecting fossil fuels several alternatives have been developed, but only a few competitors have remained that offer basically equal characteristics in contrast to conventional fuel. According to global trends in aviation, the National University of Public Service has also decided about the introduction of alternative fuel for the companies of state aviation. The main aim of this paper is to investigate the effect of different fuel brands on the operational behavior of the gas turbine engines through independent methods involving simplified meanline calculations, complex CFD simulations and measurements carried out on a turbojet engine test bench. The theoretical aspects of the assessment focuses on steady state performance only, while the survey of the real gas turbine engine includes transient situations like acceleration, deceleration and starting as well. Reference measurements have been carried out with conventional Jet-A1 fuel, then synthetic and bio fuels have been tested. The operational range of the engine involved in the study covers the entire envelope from idling conditions up to takeoff thrust. However, because the test bench is ground-based, such analysis like reignition capability of the fuels at high altitude have been tested in an independent special laboratory. Even if it does not count to the primary objectives of military aviation, the authors have conducted evaluation of emissions from the different fuels, taking into account the possible roles of fixed and rotary winged aircraft. As a conclusion of the performed investigations, it can be stated that alternative jet engine fuels offer equal performance and safety levels like traditional ones, but long-term effects on the service life of the engine as well as system costs including storage, infrastructure, etc. can have disadvantages.