The propulsion demands of high speed naval vessels often rely on gas turbines fitted in small engine rooms, producing significant amounts of power achieving thus high performance requirements. Gas turbines can be used either to provide purely mechanical propulsion, or alternatively to generate electricity, which is subsequently used by electric drives to propel the ship. However, the thermal efficiencies of gas turbines are lower than those of Diesel engines of similar power, in addition to the fact that all gas turbines are less efficient as the ambient temperature rises, particularly for aero-derivative engines. In the context of improving the performance of existing marine gas turbines with minimum modifications to their baseline configuration, this article is proposing engine’s performance enhancement by integrating a pressure wave supercharger (or wave rotor), while keeping the compressor, combustion chamber and turbine entry temperature of the baseline engine unchanged. Thermodynamic cycle analysis for two-shaft gas turbine engines configurations with and without heat exchanger to recuperate the waste heat from the exhaust gases, typical for marine propulsion is performed for the baseline engines, as well as for the topped with four-port wave rotor engines, at design point conditions and their performances are compared accordingly. Important benefits are obtained for four-port wave rotor-topped engines in comparison to the self-standing baseline engines for the whole range of engine’s operation. It is found that the higher the turbine inlet temperature is, the more the benefit gain of the wave rotor topped engine is attained in terms of efficiency and specific power. It is also concluded that the integration of wave rotor particularly favours engines operating at low compressor pressure ratios and high turbine inlet temperatures. The effect of variation of the most important parameters on performance of the topped engine is investigated. It is concluded that wave rotor topping of marine gas turbines can lead to fuel savings and power increase.