This paper presents the development of a real-time Supervision Hardware-in-the-Loop (HIL) emulator of shaded PV systems. This study is focused on shaded conditions due to the impact of shadows in the final energy production and the global structural healthy. In this context, we propose a methodology to emulate in real-time the shaded PV system behavior. This proposed methodology is intended for evaluation of supervision and fault detection strategies using a Hardware-in-the-Loop approach. This study takes advantage of FPGAs given their features of adaptability and parallel processing suitable for emulation of complex shaded PV systems. The proposed methodology employs the High Level Specification of Embedded Systems (HiLeS) for automatic VHDL code generation, and the graphical Systems Modeling Language (SysML) to represent the PV system behavior. Experimental results show the emulation of current-voltage behavior of PV modules under normal and shaded conditions. Emulation results are compared with experimental and conventional computational approaches shown a high degree of accuracy.