Thermoacoustic system is a system introduced as an alternative technology for refrigerators or heat engine because it uses environmentally friendly gases as a working medium. Thermoacoustic system usually uses noble gaseous as working medium and air has been widely used since it is available abundantly and easy to handle when performing experiment. Other than air, helium is also frequently used in thermoacoustic system because its low Prandtl number is expected to improve the performance of thermoacoustic system. This paper reports the computational results of heat transfer performance across tube banks heat exchanger when air and helium are used in thermoacoustic environment. The transient cases of thermoacoustics were solved using the Shear-Stress-Transport k-ω turbulence model. The model was first validated with experimental results with air as the working fluid. The validated model was then solved for helium. Results showed that helium offers higher Nusselt number (6.52%) and Colburn-j factor (11.25%) compared to air at lower Reynolds number. Hence, the study suggests that the use of helium gas is favorable if better heat transfer is to be achieved in thermoacoustic energy system.