Abstract Background: An accurate prognostic prediction can improve the individualized management of patients with pancreatic cancer (PC), and the exploration of biomarkers with prognostic value for clinical practice is the prerequisite of the work. Butyrophilin-Like 9 (BTNL9) has recently been found to function as a tumor suppressor gene in a variety of malignancies and has the potency to serve as a prognostic biomarker. Our aim was to explore the relationship between BTNL9 expression and the prognosis of PC, and to unearth its upstream and downstream molecular mechanisms. Methods: The RNA expression of BTNL9 was analyzed in 5 datasets from Gene Expression Omnibus (GEO) database. The protein expression of BTNL9 was detected by immunohistochemistry in a cohort including 42 PC patients. The relationship between BTNL9 expression and prognosis was analyzed by survival and prognostic factors analysis. Online database and Gene Set Enrichment Analysis (GSEA) were used to explore the upstream and downstream molecular mechanisms of BTNL9. Correlation analysis and CIBERSORT were applied to investigate the relationship between BTNL9 and tumor immunology.Results: In multiple datasets and our cohort, BTNL9 expression was decreased in PC tissues. Patients with high expression of BTNL9 had a better prognosis. BTNL9, age and N stage were identified as the independent prognostic factors of PC. BTNL9 was predicted to be down-regulated by hsa-miR-1910-5p, and it may be involved in the proteasome and PC signaling pathway. Interestingly, genes of proteasome (PSMD2, PSMD7 and PMSD14) and deubiquitin system (USP20, USP27X and USP30) combined BTNL9 could improve the prognostic prediction of PC. In addition, the expression of BTNL9 correlates with the expression of immune checkpoints and influences the infiltration of tumor immune cells. Conclusions: BTNL9 can serve as a prognostic marker of PC, and high expression of BTNL9 was generally associated with better prognosis. Combined the expression of BTNL9 and the expression of PSMD2, PSMD7, PMSD14, USP20, USP27X and USP30 can more accurately analyze the prognosis of patients with PC.