In the treatment of ischemic stroke, much attention is paid to neuroprotective therapy aimed at maintaining the viability and restoring the functions of nervous system cells. The peptide Selank (Thr-Lys- Pro-Arg-Pro-Gly-Pro) is an analog of endogenous tuftsin and is used as a drug that affects the human nervous system. Selank exerts anxiolytic, nootropic, neuroprotective, and immunomodulatory effects. However, its neuroactivity may be broader and manifest itself in conditions of severe damage to neurological functions, such as stroke. A magnetic resonance imaging-guided transient middle cerebral artery occlusion (tMCAO) model was used to investigate the Selank-induced gene expression changes in the rat brain in the early hours after ischemia. High-throughput RNA sequencing of the rat frontal cortex was performed 4.5 h after tMCAO, and 118 differentially expressed genes (DEGs) with a fold change of >1.5 and Padj < 0.05 were identified after Selank administration compared with saline administration. Most of the DEGs (99) were downregulated in response to Selank. Of these, 60 DEGs (C1qc, RT1-Ba, Cd68, Cd74, etc.) were upregulated by ischemia alone. Thus, Selank significantly reduced the ischemia-induced disturbances in the expression profile of the genes, showing a compensatory effect. Further functional analysis (GSEA) revealed Selank activity towards genes involved in neuroreception and immunity, including antigen processing and presentation and the complement system. Thus, Selank was found to regulate ischemic damage-induced processes at the molecular genetic level.