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Blue gourami (gourami, Trichogaster trichopterus) is a model for labyrinth fishes (Anabantoidei) adapted to partial air breathing. Its reproductive endocrinology has been extensively studied, and transcriptomic sex differences in the gonads were described. Nevertheless, sex differences in gene expression in non-gonadal tissues ostensibly affected by the sex-specific hormonal balance, e.g., the brain, are unknown. To assess such differences, we used bulk RNA-seq to assemble and compare polyA+ transcriptomes between whole brains of four adult male and five adult female gourami, in addition to other tissues (three dorsal fin and five ovary samples) from the same female group. While all nine brain transcriptomes clustered together relative to the other tissues, they showed separation according to sex. A total of 3568 genes were differentially expressed between male and female brains; of these, 1962 and 1606 showed lower and higher expression in males, respectively. Male brains showed stronger down-regulation of specific genes, which included hormone receptors, e.g., pituitary adenylate cyclase-activating polypeptide receptor (pacap-r1). Among the genes with lower expression in male brains, multiple pathways essential to brain function were over-represented, including GABA, acetylcholine and glutamate receptor signaling, calcium and potassium transmembrane transport, and neurogenesis. In contrast, genes with higher expression in male brains showed no significant over-representation of brain-specific functions. To measure the mRNA levels of specific hormone receptors known from prior studies to regulate reproductive function and behavior in gourami and to validate RNA-seq results for these specific genes, we performed RT-qPCR for five receptors, pacap-r1, gonadotropin-releasing hormone 2 receptor (gnrh2r), kisspeptin receptor 1 (gpαr1/kiss1), insulin-like growth factor 1 receptor (igf1r), and membrane progesterone receptor 1 (mpr1), in the brain RNA sample groups. Of these, pacap-r1 showed a significant, three-fold down-regulation, while gpαr1/kiss1 showed a significant two-fold down-regulation in male vs. female gourami brains. Our results are novel in describing the suppression of brain function-related gene expression in male, as compared to female, gourami brains. Further research is needed to assess the behavioral significance of this effect and its prevalence in other vertebrate groups. [ABSTRACT FROM AUTHOR]