Objective To investigate the transcriptomics characteristics of splenic T follicular helper (Tfh) cells in mice infected with Schistosoma japonicum, and to screen and validate key differentially expressed genes (DEGs), so as to unravel the potential regulatory role of Tfh cells in the immune response to S. japonicum infection. Methods C57BL/6 mice were randomly divided into an infection group and a control group, of 8 mice each group. Mice in the infection group were infected with S. japonicum cercariae via skin contact, while animals in the control group received no treatment. Mouse spleens were sampled 6 weeks post-infection, and Tfh cells were isolated by gating based on the immune phenotype of positive cluster of differentiation 3, cluster of differentiation 4, CXC subfamily receptor 5, programmed death-1 (CD3⁺ CD4⁺ CXCR5⁺ PD-1⁺) by means of negative selection with magnetic beads and flow cytometry. Total RNA was extracted from cell samples with an RNA extraction kit and purified. Bulk RNA-seq sequencing was performed on the Illumina platform to screen DEGs [|log₂FoldChange| > 1 and P < 0.05], and DEGs were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, and screened DEGs were validated using reverse transcription quantitative Real-time PCR (RT-qPCR) assay. The expression of interleukin 5 (IL-5) and IL-13 proteins was measured using enzyme-linked immunosorbent assay (ELISA) in the serum of mice 2, 4, 6 and 8 weeks post-infection. Results Transcriptome sequencing identified a total of 1 379 DEGs, including 327 upregulated and 1 052 downregulated genes. GO and KEGG functional enrichment analyses revealed that these genes were significantly enriched in signal pathways of cytokine-cytokine receptor interaction, chemotaxis, and immune effector process regulation. RT-qPCR assay quantified higher relative il5 [(13.520 ± 1.540) vs. (1.060 ± 0.225); t = 10.52, P < 0.01] and il13 mRNA expression [(22.930 ± 0.720) vs. (1.137 ± 0.425); t = 28.41, P < 0.01] in the infection group than in the control group, and showed no significant difference between the infection and control groups in terms of relative neuromedin U receptor 1 (nmur1) [(11.210 ± 4.480) vs. (1.007 ± 0.084); t = 3.054, P > 0.05] or prostaglandin D2 receptor 2 (ptgdr2) mRNA expression [(4.405 ± 2.575) vs. (1.143 ± 0.443); t = 1.629, P > 0.05]. ELISA measured extremely low IL-5 (median, 2.00 pg/mL) and IL-13 concentrations (median, 4.00 pg/mL) in both uninfected mice and at early stages of infections (2 weeks post-infection). The median IL-13 concentration increased to 68.20 pg/mL at 4 weeks post-infection (P < 0.05), and the median IL-5 concentration rose to 77.06 pg/mL at 6 weeks post-infection (P < 0.05), which was maintained a high level in subsequent infection phases. Conclusion S. japonicum infection remarkably reshapes the transcriptome profile of murine splenic Tfh cells, leading to a highly activation state. Tfh cells may participate in maintaining the host Th2-type immune microenvironment and regulating immunopathology through significantly upregulating il5 and il13 expression.