With the growing complexity in consumer embedded products and the improvements in process technology, Multi-Processor System-On-Chip (MPSoC) architectures have become widespread. These new systems are complex to design as they must execute multiple complex applications (e.g. video processing, 3D games), while meeting additional design constraints (e.g. energy consumption or time-to-market). Moreover, the rise of temperature in the die for MPSoC components can seriously affect their final performance and reliability. Therefore, mechanisms to efficiently evaluate complete HW/SW MPSoC designs in terms of energy consumption, temperature, performance and other key metrics are needed. In this paper, we present a new HW/SW FPGA-based emulation framework that allows designers to rapidly extract a number of critical statistics from processing cores, memories and interconnection systems being emulated on a FPGA. This information is then used to interact in real-time with a SW thermal model running on a host computer via an Ethernet port. The results show speed-ups of three orders of magnitude compared to cycle-accurate MPSoC simulators, which enable a very fast exploration of a large range of MPSoC design alternatives at the cycle-accurate level. Finally, our HW/SW framework allows designers to test run-time thermal management strategies with real-life inputs without any loss in the performance of the emulated system.