In this paper design of fuzzy logic controller (FLC) on system on chip field programmable gate array (SoC FPGA) for Shell and Tube Heat Exchanger (STHE) is described. STHE is interfaced with Compact Reconfigurable Input Output (CRIO) based FPGA through data acquisition (DAQ) card. For designing controller on chip, National Instruments (NI) CRIO-9101 is reconfigured with FLC code. Interfacing is carried out with NI analog input-output device embedded with NI CRIO-9012 microcontroller and NI CRIO-9101 FPGA module. A graphical program is developed for real-time control of the process plant using CRIO based FPGA. FPGA acts as a standalone processor instead of PC for controlling the STHE. The fuzzy logic controller designed on FPGA is compared with benchmark controller in real time temperature control of STHE. It is demonstrated that the controller proposed outperformed conventional controller.