A polysaccharide of Irpex lacteus, a white‐rot fungus with lignocellulose‐degrading activities, has been used as a commercial medicine for nephritis treatment. Previously, a low‐intensity electromagnetic field (LI‐EMF) was found to increase the biomass and polysaccharide content of Irpex lacteus and induce twists on the cell surface. In this study, RNA‐sequencing (RNA‐seq) technology was used to analyze the underlying mechanism of LI‐EMF's influence on Irpex lacteus. We identified 3268, 1377, and 941 differentially expressed genes (DEGs) in the LI‐EMF‐treated samples at recovery times of 0 h, 3 h, and 6 h, respectively, indicating a significant decline in the influence of the LI‐EMF treatment on Irpex lacteus with the passage of recovery time. Moreover, 30 upregulated and 14 downregulated DEGs overlapped in the LI‐EMF‐treated samples at the recovery times of 0 h, 3 h, and 6 h, implying the important lasting effects of LI‐EMF. The reliability of the RNA‐seq data were validated by quantitative real‐time PCR (qRT‐PCR). The DEGs related to transcription factors, cell proliferation, cell wall, membrane components, amino acid biosynthesis and metabolism, and polysaccharide biosynthesis and metabolism were significantly enriched in the LI‐EMF‐treated samples. The experiments confirmed that the LI‐EMF treatment significantly increased the content of amino acids with a considerable increase in the content of essential amino acids. Therefore, the global gene expression changes explained the pleiotropic effects of Irpex lacteus induced by the LI‐EMF treatment. These findings provide the requisite data for the appropriate design and application of LI‐EMF in the fermentation of microorganisms to increase production. Bioelectromagnetics. 40:104–117, 2019. © 2019 Bioelectromagnetics Society