In this paper, a post-analysis of cooling system for infrared(IR) window was performed based on heating experiment of IR window system. We applied the same experimental conditions to analysis, and then validated the analysis technique by comparing numerical and experimental results. For an analysis software, we used a professional heat/fluid analysis program and the numerical and experimental results were in fairly good agreement. We investigated the effect of thermal transfer between the frame and IR window and also a cooling efficiency between fluid and structure in order to determine the proper parameters for the analysis. In this study, 100 % thermal transfer between the frame and IR window and 30 % cooling efficiency between fluid and structure have been proposed, which can be used in the future conceptual design and analysis of similar IR windows.