Double pane window system, in which an air layer with a finite width is filled between glasses, is used in order to increase the insulation efficiency. In the present study, a conjugate heat transfer problem of a double pane window system has been studied numerically in order to investigate the effect of an air layer on the heat transmittance of the double pane window system using a finite element method based on P2P1 basis function. In this study on the conjugate heat transfer of a double pane window system, numerically predicted Nusselt numbers with or without conjugate heat transfer effect have been compared with an available existing empirical formula. It has been found that a Nusselt number from an existing formula for an enclosed space is different from that obtained from the present conjugate heat transfer analysis mainly due to the effects of a very high aspect ratio and conjugate heat transfer mechanism. Furthermore, it has been shown that the numerically estimated optimal air thickness of the double pane window system with conjugate heat transfer effect is a little bit longer than that obtained without considering conjugate heat transfer effect.