This book constitutes the thoroughly refereed post-workshop proceedings of the Third International Workshop on Modelling and Simulation for Autonomous Systems, MESAS 2016, held in Rome, Italy, in June 2016. The 33 revised full papers included in the volume ware carefully reviewed and selected from 38 submissions. They are organized in the following topical sections: human machine integration and interfaces; autonomous systems and MS frameworks and architectures; autonomous systems principles and algorithms; unmanned aerial vehicles and remotely piloted aircraft systems; modelling and simulation application. .