There are few studies on the use of PEF for treating A. niger. In this study, we used a self-designed PEF treatment system to investigate the effects of different electrical parameters of PEF (electric field strength of 5–20 kV/cm and treatment time of 1–10 ms) on the germination of A. niger spores, as well as the activity of its lipase and glucoamylase. We aimed to identify the optimal promotion parameters and analyze the reasons for the promotion of their activity by PEF.