In this study, we used high-throughput technology to provide the first transcriptome dataset for differentially expressed genes in mixed pools of dominant and nondominant follicles of goats. These data will contribute to research on the molecular mechanisms of dominant follicle selection in goats. In this study, 90276370 and 115579236 clear reads in dominant and nondominant follicles of goat were generated through Illumina paired-end sequencing, and their mapping rate was 84.99% and 84.47%, respectively. A total of 12577 differentially expressed genes (DEGs) were identified, including 6009 upregulated and 6568 downregulated genes in dominant follicles compared with nondominant follicles of goat. Of the 1026 significantly differentially expressed, long noncoding RNAs (lncRNAs) found, 419 were upregulated and 607 were downregulated. The DEGs related to 56 GO categories, and pathway analysis revealed that these DEGs were significantly enriched in 41 of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including signaling pathways regulating the pluripotency of stem cells, the p53 signaling pathway, and oxidative phosphorylation. The results of the present study confirmed that the selection of the dominant follicle involved the regulation of various physiological systems. These results provided helpful data to understand on the molecular mechanisms of dominant follicle selection in goats.