Pancreatic ductal adenocarcinoma (PDAC) is a very aggressive cancer, with low survival rates and limited therapeutic options. Thus, the elucidation of signaling pathways involved in PDAC pathogenesis is essential to identify novel potential therapeutic gene targets. Here, we used a systems approach by integrating gene and microRNA profiling analyses together with CRISPR/Cas9 technology, to identify novel transcription factors involved in PDAC pathogenesis. FOXA2 transcription factor was found to be significantly down-regulated in PDAC relative to control pancreatic tissues. Functional experiments revealed that FOXA2 has a tumor suppressor function through inhibition of pancreatic cancer cell growth, migration, invasion and colony formation. In situ hybridization analysis revealed miR-199a significantly upregulated in pancreatic cancer. Bioinformatics and luciferase analyses showed that miR-199a negatively regulates directly FOXA2 expression, through binding in its 3' untranslated region (UTR). Evaluation of the functional importance of miR-199 on pancreatic cancer revealed that miR-199 acts as an inhibitor of FOXA2 expression, inducing an increase in pancreatic cancer cell proliferation, migration and invasion. Additionally, gene ontology and network analyses in PANC-1 cells treated with an siRNA against FOXA2 revealed an enrichment for cell invasion mechanisms through PLAUR and ERK activation. FOXA2 deletion (FOXA2) by using two CRISPR/Cas9 vectors in PANC-1 cells, induced tumor growth in vivo, resulting in up-regulation of PLAUR and ERK pathways in FOXA2 xenograft tumors. Taken together, we have identified FOXA2 as a novel tumor suppressor in pancreatic cancer, regulated directly by miR-199a, enhancing our understanding on how microRNAs interplay with the transcription factors to affect pancreatic oncogenesis.