Recently, we found anovulation in nuclear progestin receptor (Pgr) knockout (Pgr-KO) zebrafish, which offers a new model for examining Pgr regulated genes and pathways that are important for ovulation and fertility. In this study, we examined expression of all transcripts using RNA-Seq in pre-ovulatory follicular cells collected after the final oocyte maturation, but prior to ovulation, from wild-type (WT) or Pgr-KO fish. Differential expression analysis revealed 2,888 genes significantly differentially expressed between WT and Pgr-KO fish. Among those, 1,230 gene transcripts were significantly more expressed, while 1,658 genes were significantly less expressed in WT than those in Pgr-KO. We then retrieved and compared transcriptional data from online databases and further identified 661 conserved genes in fish, mice, and humans, that showed similar levels of high (283 genes) or low (387) expression in animals that were ovulating compared to those with no ovulation. For the first time, ovulatory genes and their involved biological processes and pathways were also visualized using Enrichment Map and Cytoscape. Intriguingly, enrichment analysis indicated the genes with higher expression were involved in multiple ovulatory pathways and processes such as inflammatory response, angiogenesis, cytokine production, cell migration, chemotaxis, MAPK, focal adhesion, and cytoskeleton reorganization. In contrast, the genes with lower expression were mainly involved DNA replication, DNA repair, DNA methylation, RNA processing, telomere maintenance, spindle assembling, nuclear acid transport, catabolic processes, nuclear and cell division. Our results indicate that a large set of genes (>3,000) are differentially regulated in the follicular cells in zebrafish prior to ovulation, terminating programs including growth and proliferation, and beginning processes including the inflammatory response and apoptosis. Further studies are required to establish relationships among these genes and an ovulatory circuit in zebrafish model.