Beta-1,3-N-acetylglucosaminyltransferase-3 (B3GNT3) is a carcinogenic factor in many cancers. However, the biological functions of B3GNT3 in gynecologic cancers especially in cervical, ovarian, and endometrial cancers are mostly limited. B3GNT3 levels in pan-cancer and gynecologic cancers were predicted by GSCA, GEPIA, and the Human Protein Atlas databases. The overall survival was predicted by Kaplan-Meier Plotter. ROC curve was generated according to the TCGA database. The immune cell infiltration was analyzed by ImmuCellAI algorithm using GSCA database. The related genes and pathways were analyzed via LinkedOmics portal, GO, KEGG pathway enrichment analysis, and GEPIA database. B3GNT3, p-p65/p65, and nuclear p65 levels were detected by western blotting. B3GNT3 was differentially expressed in pan-cancers. B3GNT3 expression was increased in cervical, ovarian, and endometrial cancers. High expression of B3GNT3 was associated with lower overall survival, and was used for diagnosis of these gynecologic cancers. B3GNT3 was related to different immune cell infiltration. B3GNT3 was associated with NF-κB signaling activation by regulating multiple related biomarkers. Silencing of B3GNT3 repressed activation of the NF-κB signaling in gynecologic cancers. In conclusion, upregulated B3GNT3 is related to diagnosis, poor prognosis, immune infiltration, and activation of the NF-κB signaling in gynecologic cancers.