Objective To screen the differentially expressed genes (DEGs) by comparing the transcriptome of the brain tissues between the mice chronically infected with Toxoplasma gondii and normal mice, to analyze the relative transcription level of DEGs in the depression-related kynurenine (KYN) pathway and to provide a theoretical basis for exploring the mechanism of depression-like symptoms caused by Toxoplasma gondii chronic infecttion in mice. Methods SV129 male mice (n = 18) were randomly and equally divided into the infection group and the control group. Mice in the infection group were intraperitoneally injected with 120 tachyzoites of T. gondii ME49 strain (200 μl), and mice in the control group were injected with the same volume of PBS. After 3 months post-infection, mice brain tissues of the two groups were collected for extraction of total RNA to undertake transcriptome sequencing for screening DEG. With the DEGs obtained, cluster analysis, gene ontology (GO) functional annotation analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation and enrichment analysis were performed. Eight DEGs [interferon-γ (IFN-γ), indoleamine 2,3-dioxygenase 1 (IDO1), IDO2, kynurenine-3-monooxygenase (KYNU), kynurenine-3-monooxygenase (KMO), 3-hydroxyanthranilate 3,4-dioxygenase (3-HAO), vimentin (Vim) and brain-derived neurotrophic factor (BDNF)] related to KYN pathway associated with depression were selected to examine each gene’s relative transcription level by quantitative real-time PCR (qRT-PCR), using glyceraldehyde-3-phosphate dehydrogenase gene as an internal reference. Results Transcriptome sequencing found 2 295 DEGs in the brain of the mice from the infection and control groups, of which 2 016 were up-regulated and 279 were down-regulated. GO analysis showed that localisation was the most significantly enriched biological process, with a total of 257 DEGs. The most significantly enriched in cellular components was the protein-containing complex, with a total of 425 DEGs. The most significantly enriched molecular function was molecular transducer activity, with 177 DEGs. The largest number of DEGs enriched in biological process, cell component and molecular function were cell process, cell part and binding, with 1 039, 1 240 and 1 088 DEGs, respectively. KEGG analysis showed that the top three up-regulated metabolic pathways were the immune system, signaling transduction, and viral infectious disease, and the top three down-regulated pathways were signal transduction, signaling molecules and interaction and immune system. Functional enrichment analysis showed that 77 pathways were significantly enriched. The signaling pathways related to depression include tumor necrosis factor signaling pathway, neuroactive ligand-receptor interaction, NF-kappa B signaling pathway, JAK-STAT signaling pathway, necroptosis, apoptosis, chemokine signaling pathway, KYN pathway. The qRT-PCR results showed that the relative transcription levels of IFN-γ, IDO1, IDO2, KYNU, KMO, 3-HAO and Vim genes in the infection group were 3 023.08%, 355.52%, 190.17%, 496.55%, 339.92%, 212.74% and 507.34%, if the relative transcript level of control mice was taken as 100%. Compared with the control group, the transcription was significantly up-regulated (t = 3.782, 3.749, 3.226, 2.908, 2.533, 5.656, 2.948; all P < 0.05 or 0.01). The relative transcription level of BDNF was 63.32%, which was significantly down-regulated (t = 2.398, P < 0.05). The fold change of IFN-γ, IDO1, IDO2, KYNU, KMO, 3-HAO, BDNF, Vim obtained by qRT-PCR was 4.96, 1.74, 0.89, 2.10, 1.60, 1.06, -0.94, 2.18, respectively. The fold change obtained by transcriptome sequencing was 7.30, 0.55, 0.80, 3.83, 2.75, 3.53, -0.86 and 1.93, respectively. The transcriptional trend obtained by qRT-PCR was consistent with that obtained by transcriptome sequencing. Conclusion DEGs from brain tissues of mice chronically infected with T. gondii were screened. Transcriptome analysis revealed that the immune response of central nervous system of the mice with chronic infection of T. gondii was continuously activated. Seven DEGs in KYN pathway related to depression showed up-regulated transcription level.