Coolants play a major role in the performance of heat exchanging systems. In a marine gas turbine engine, an intercooler is used to reduce the compressed gas temperature between the compressor stages. The thermophysical properties of the coolant running within the intercooler directly influence the level of enhancement in the performance of the unit. Therefore, employing working fluids of exceptional thermal properties is beneficial for improving performance in such applications, compared to conventional fluids. This paper investigates the effect of utilizing nanofluids for enhancing the performance of a marine gas turbine intercooler. Multi-walled carbon nanotubes (MWCNTs)-water with nanofluids at 0.01–0.10 vol % concentration were produced using a two-step controlled-temperature approach ranging from 10 °C to 50 °C. Next, the thermophysical properties of the as-prepared suspensions, such as density, thermal conductivity, specific heat capacity, and viscosity, were characterized. The intercooler performance was then determined by employing the measured data of the MWCNTs-based nanofluids thermophysical properties in theoretical formulae. This includes determining the intercooler effectiveness, heat transfer rate, gas outlet temperature, coolant outlet temperature, and pumping power. Finally, a comparison between a copper-based nanofluid from the literature with the as-prepared MWCNTs-based nanofluid was performed to determine the influence of each of these suspensions on the intercooler performance.