This thesis represents the synthesis of almost two years of work within the CubeSat team at the Polytechnic University of Turin, and its scope is to illustrate the development of a user-friendly, multi-functional simulator for small satellites. This simulator, called by the proprietary name of StarSim v2.0, will have to perform at least three different kinds of in-the-loop simulation: Algorithm-in-the-loop, Software-in-the-loop and Hardware-in-the-loop, and each of these has to be consistent with the previous ones. In the first chapter, a general introduction to System Engineering is provided, completed with the necessary knowledge to Model-Based Design and Validation techniques, upon which all the rest of this work is based.