Fusarium oxysporum f. sp. cubense race 4 (Foc4), the strong virulent pathogen of Banana Fusarium Wilt, must face to oxidative burst produced by the host in the early stage of infecting banana plants. [Objective] To study the molecular mechanism how Foc4 responses exogenous oxidative stress, [Methods] RNA-Seq was done between the wild type B2 strain of Foc4 treated by H₂O₂ and the control using Illumina 2500 sequencing platform, and differentially expression genes (DEGs) was analyzed. [Results] The growth of Foc4 was inhibited under exogenous oxidative stress, and more than 20 million clean reads were obtained after RNA-Seq. Compared with the control, a total of 496 genes were up-regulated and 298 genes were down-regulated, respectively, with FDA value ≤ 0.001 and Fold Change (FC) ≥ 2 used as the selection criteria. Gene ontology (GO) functional enrichment analysis showed that 429 genes were annotated in the GO functional analysis database. Many of them were related to metabolic processes, biological regulation, cellular processes and response to stimuli. Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis showed that 141 DEGs were annotated in 50 metabolic pathways in KEGG. These metabolic pathways mainly include the metabolic pathway of various amino acids and fatty acid. It also includes metabolic pathways that are directly related to antioxidant stress, including damage repair of DNA, biosynthesis of carotenoids, peroxisome and glutathione metabolism. [Conclusion] Material metabolism, energy metabolism and signal regulation pathways directly dealing with oxidative stress must be changed in Foc4 cells to cope with environmental stress and to survive in strong oxidative stress environment.