The present invention provides a FPGA circuit fault detection device, including an input signal encoder, an output signal encoder, at least one fault probe, and a fault positioner. The input signal encoder is used for processing time redundancy encode to the input signal; the output signal encoder is used for ensuring the detected FPGA circuit output correct result; the fault probe is used for processing time redundancy encode to the output of any point of the detected FPGA circuit, comparing the output result of the same input on the different time nodes, judging the detected FPGA circuit fault. The FPGA circuit fault detection device further includes a fault positioner, used for encoding the output result of the fault probe, locating the fault in a smaller local area. The device not onlyquickly detects the fault, but also having less system cost, simple realization.