Background: Pancreatic carcinoma (PC) is one of the most aggressive cancers affecting human health. Identifying candidate biomarkers is essential for the early diagnosis and good prognosis of PC. Fibronectin type III domain containing 3B (FNDC3B) promotes many types of cancer, but its role in pancreatic cancer is not clear. The purpose of this study was to investigate the relationship between the expression of FNDC3B and incidence of PC. Methods: We downloaded data related to the levels of FNDC3B mRNA in patients of PC from the Cancer Genome Atlas (TCGA) database, and conducted in-depth research on this data and its clinical significance through the R tools. We used GO and KEGG enrichment analyses to study the genes and signaling pathways that may be regulated by FNDC3B. Results: The results showed that the level of FNDC3B mRNA in PC tissues was higher than that in the normal tissues, and this was associated with proliferation and lymph node metastases of PC. Increased levels of FNDC3B mRNA also predict poor prognosis for the patients with PC. In addition, enhanced levels of FNDC3B mRNA were involved in the regulation of cell junction, tissue and epithelial cell migration, and several signal transduction pathways, including notch, TGF-β, VEGF, and Wnt. Conclusions: In short, high levels of FNDC3B mRNA may be associated with progression of PC and indicate a poor prognosis in patients with PC.