Chromatin remodeling is a known mechanism of drug resistance in pancreatic ductal adenocarcinoma (PDAC). Here, we demonstrate that overexpression of HDAC1, a gene encoding a histone deacetylase involved in several chromatin remodeling complexes, is associated with multi-drug resistance and patient survival in PDAC. We characterized the effects of HDAC1 overexpression in a pancreatic cancer cell line using transcriptomics and ChIP-seq for HDAC1 and H3K27 acetylation. These data showed that HDAC1 overexpression results in a more stem-like state and contributes to chemoresistance in PDAC. We identified HDAC1 target genes and used them to develop a clinically relevant nine-transcript signature that predicts patient prognosis. One downstream consequence of HDAC1 overexpression is GTPase activity, thus nominating GTPases as therapeutic drug targets with the potential to reverse chemoresistance. These findings nominate novel drug targets and propose a novel therapeutic tool to improve patient care.