A novel method for square wave pulse shaping based on field-programmable gate array (FPGA) is proposed. Aiming at the waveform distortion problem of square wave pulses caused by an erbium-doped fiber amplifiers (EDFA), a high-quality square wave pulse with a repetition frequency of 91.27 kHz and a pulse width of 650 ns is successfully obtained by using an extra-cavity pulse-shaping system. The experimental results show that the system can effectively suppress the distortion caused by gain saturation during the amplification process of the square pulse, and the consistency between the spectral envelope of the square pulse after shaping and the sinc function envelope of the ideal square wave pulse is significantly enhanced. This study applies FPGA to distortion correction after amplification of square pulses with a pulse width of hundreds of nanoseconds, and the results can provide technical support for the acquisition of high-energy and high-quality square wave pulses, and further promote their wide application in fields such as supercontinuum generation.