We develop a model of wave propagation through the upper atmosphere taking into account the thermospheric collision frequencies and the Faraday rotation. We use this model to numerically test the effect of these collisions on the Global Positioning System (GPS) signal between 50 and 1000 km altitude. We study several characteristics of the GPS wave: ionospheric delay, dephasing, and variation of amplitude. We point out that the thermosphere influence is negligible, about 10-9 m on ionospheric delay, and may be considered as negligible on shorter-frequency waves. This study is extended to satellite-to-satellite communications both for quiet and magnetic storm cases. In this case the influence on the wave is greater but remains very weak.