Introduction: Cerebral malaria (CM) is a lethal neuroinflammatory disease caused by Plasmodium infection. Immune cells and brain parenchyma cells contribute to the pathogenesis of CM. However, a systematic examination of the changes that occur in the brain parenchyma region during CM at the single‐cell resolution is still poorly studied. Aims: To explore cell composition and CD8+ T cell infiltration, single‐cell RNA sequencing (scRNA‐seq) was performed on the brainstems of healthy and experimental cerebral malaria (ECM) mice. Then CD8+ T cell infiltration was confirmed by flow cytometry and immunofluorescence assays. Subsequently, the characteristics of the brain‐infiltrated CD8+ T cells were analyzed. Finally, the interactions between parenchyma cells and brain‐infiltrated CD8+ T cells were studied with an astrocytes‐CD8+ T cell cocultured model. Results: The brainstem is the most severely damaged site during ECM. ScRNA‐seq revealed a large number of CD8+ T cells infiltrating into the brainstem in ECM mice. Brain‐infiltrated CD8+ T cells were highly activated according to scRNA‐seq, immunofluorescence, and flow cytometry assays. Further analysis found a subset of ki‐67+ CD8+ T cells that have a higher transcriptional level of genes related to T cell function, activation, and proliferation, suggesting that they were exposed to specific antigens presented by brain parenchyma cells. Brain‐infiltrated CD8+ T cells were the only prominent source of IFN‐γ in this single‐cell analysis. Astrocytes, which have a high interferon response, act as cross‐presenting cells to recruit and re‐activate brain‐infiltrated CD8+ T cells. We also found that brain‐infiltrated CD8+ T cells were highly expressed immune checkpoint molecule PD‐1, while parenchyma cells showed up‐regulation of PD‐L1 after infection. Conclusions: These findings reveal a novel interaction between brain‐infiltrated CD8+ T cells and parenchyma cells in the ECM brainstem, suggesting that the PD‐1/PD‐L1 signal pathway is a promising adjunctive therapeutic strategy for ECM targeting over‐activated CD8+ T cells. [ABSTRACT FROM AUTHOR]