The peanut (Arachis hypogaea) is an important crop species that is threatened by drought stress. The genome sequences of peanut, which was officially released in 2016, may help explain the molecular mechanisms that underlie drought tolerance in this species. We report here a gene expression profiling of A. hypogaea to gain a global view of its drought resistance. Using whole-transcriptome sequencing, we analysed differential gene expression in response to drought stress in the drought-resistant peanut cultivar J11. Pooled samples obtained at 6, 12, 18, 24, and 48 h were compared with control samples at 0 h. In total, 51,554 genes were found, including 49,289 known genes and 2265 unknown genes. We identified 224 differentially expressed transcription factors, 296,335 SNPs and 28,391 InDELs. In addition, we detected significant differences in the gene expression profiles of the treatment and control groups. After comparing the two groups, 4648 genes were identified. An in-depth analysis of the data revealed that a large number of genes were associated with drought stress, including transcription factors and genes involved in photosynthesis-antenna proteins, carbon metabolism and the citrate cycle. The results of this study provide insights into the diverse mechanisms that underlie the successful establishment of drought resistance in the peanut, thereby facilitating the identification of important genes in the peanut related to drought management. Transcriptome analysis based on RNA-Seq is a powerful approach for gene discovery and molecular marker development for this species.