Wave rotors are unsteady flow machines that exchange energy through pressure waves. This has the potential for enhancing efficiency over a wide spectrum of applications, ranging from gas turbine topping cycles to pressure-gain combustors. This paper introduces an aerodynamic shape optimisation of a power generating non-axial micro-wave rotor turbine and seeks to enhance the shaft power output while preserving the wave rotor’s capacity to function as a pressure-exchanging device. The optimisation considers six parameters including rotor shape profile, wall thickness, and number of channels and is done using a hybrid genetic algorithm that couples an evolutionary algorithm with a surrogate model. The underlying numerical model is based on a transient, reduced-order, quasi-two dimensional computational fluid dynamics model at a fixed operating condition. The numerical results from the quasi-two-dimensional optimisation indicate that the best candidate design increases shaft power by a factor of 1.78 and imply a trade-off relationship between torque generation and pressure exchange capabilities. Further evaluation of the optimised design using three-dimensional computational fluid dynamics simulations confirms the increase in power output at the cost of increased entropy production. It is further disclosed that increased incidence losses during the initial opening of the channel to the high-pressure inlet duct compromise the shock strength of the primary shock wave and account for the decrease in pressure ratio. Finally, the numerical trends are validated using experimental data.