The feasibility of the future more-electric, hybrid-electric, and all-electric aircraft configurations will depend on a good understanding of thermal aspects early in the design. However, thermal analysis of aircraft equipment bays is typically performed at later design stages to validate if the design meets the minimal certification requirements rather than to optimize the cooling strategy. The presented work aims to provide new insight into thermal aspects in typical aircraft equipment bays. In particular, system thermal interactions, such as radiation, play a more significant role in tightly packaged bays, such as avionics bays. This paper investigates the influence of radiation on the overall system heat dissipation in two representative avionics bays. Using Computational Fluid Dynamics (CFD) simulation, combined with an analytical approach, the authors analyze the impact of several parameters, such as varying mass flow rates and distances between adjacent systems, on their thermal interaction. The results suggest that the radiative effects must be considered when the gap distance between the systems is larger than 0.1 m, the flow rate between two systems is not strong enough to have high convective heat exchanges, when the systems of interest are hidden by other systems from the ventilation sources, and when the system’s internal heat dissipation is significant. Overall, this paper’s results will contribute enhance conceptual design methods, such as the previously developed Thermal Risk Analysis, and help optimize thermal management strategies for future aircraft.