Field Programmable Gate Array (FPGA) is a reconfigurable circuit and it is used for various applications such as image processing, digital signal processing and neural network. FPGA adopts a logic circuit called Look-Up Table (LUT) as a basic circuit structure. Commonly used FPGAs have volatile characteristic because it consists of SRAM based LUT that adopts SRAM as a memory cell. Volatile FPGAs have a disadvantage in terms of power management efficiency. Variation-Tolerant NonVolatile STT-MRAM (VTNV) LUT has been studied for a nonvolatile FPGAs and it has unique characteristics that can only operate in the half clock period. Accordingly, VTNV LUT based FPGA cannot operate normally with conventional FPGA CAD tool flow. We propose FPGA CAD (Computer Aided Design) tool flow for VTNV LUT based FPGA with supporting unique characteristic of VTNV LUT, and implement a non-volatile FPGA. Through proposed FPGA CAD tool flow, non-volatile FPGA based on VTNV LUT could operate normally. Because of high parameters of VTNV LUT, experimental results show that power increases by 29% and critical path delay increases by 16%, but it’ll be improved sufficiently by future VTNV LUT researches.