The Nile tilapia (Oreochromis niloticus) displays TSD sex reversal, in which temperature during embryonic development determines the sexual fate of the individual. However, few studies have found that there is a temperature-controlled gene in brain related to sex in the Nile tilapia. In this study, the brain transcriptome of tilapia was sequenced from several brain samples of control and high temperature treated group using RNA-seq technology. We aim to identify the transient and permanent gene expression changes in Nile tilapia brain after high temperature treatment.