The male rat has been used extensively as a model for evaluating the neurophysiology of sexual behavior. However, gene expression in the brain throughout the process of sexual intercourse has yet to be elucidated. In the present study, we created a transcriptomic BodyMap by performing mRNA-Seq on brain samples from pre-copulatory control (CK), fourth intromission (CR4), ejaculation (EJ) and post-ejaculatory interval 1-min (PEI1) Sprague Dawley rats (n = 40, all male, each 10). The resulting analysis generated an average of approximately 47 million sequence reads, indicating changes in roughly 21,255 genes for each sample. Among of them, significant differences in gene expression relative to control rats were observed in the CR4 (139 genes), EJ (257 genes), and PEI1 (130 genes) groups. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis identified 22 pathway-related genes. We further identified eight important genes related to neural pathways using RT-qPCR and Western blot, ruling out the possibility of false positives. The results of the present study not only revealed the basic pattern of gene expression during male rate sexual activity but also provide preliminary data and methodology for further research regarding animal sexual activity.