Satellite systems including the Global Navigation Satellite System (GNSS) and the satellite communications (SATCOM) system provide great convenience and utility to human life including emergency response, wide area efficient communications, and effective transportation. Elements of satellite systems incorporate technologies such as navigation with the global positioning system (GPS), satellite digital video broadcasting, and information transmission with a very small aperture terminal (VSAT), etc. The satellite systems importance is growing in prominence with end users’ requirement for globally high data rate transmissions; the cost reduction of launching satellites; development of smaller sized satellites including cubesat, nanosat, picosat, and femtosat; and integrating internet services with satellite networks. However, with the promising benefits, challenges remain to fully develop secure and robust satellite systems with pervasive computing and communications. In this paper, we investigate both cyber security and radio frequency (RF) interferences mitigation for satellite systems, and demonstrate that they are not isolated. The action space for both cyber security and RF interferences are firstly summarized for satellite systems, based on which the mitigation schemes for both cyber security and RF interferences are given. A multi-layered satellite systems structure is provided with cross-layer design considering multi-path routing and channel coding, to provide great security and diversity gains for secure and robust satellite systems.