Hallmarks of neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease include oxidative stress, accumulation of unfolded proteins, and neuronal cell death. One key player in maintaining redox homeostasis and oxidative protein folding is the protein disulfide isomerase (PDI). PDI has been the focus of drug discovery studies in neurodegenerative diseases, which have reported, paradoxically, that PDI inhibition is neuroprotective in cellular disease models. This study investigated the molecular implications of PDI inhibition by examining the effect of the PDI inhibitors securinine and 16F16 on the gene expression profile of SH-SYSY neuroblastoma cells. Microarray analysis identified 36 genes that were differentially expressed in both inhibitor treatments. Computational approaches revealed that these differentially expressed genes are involved in apoptosis and cell death and that they are part of a protein-protein interaction network. Among the 36 identified genes, NAD(P)H quinone dehydrogenase 1 (NQO1) displayed the highest average expression change. As a central player in the cellular oxidative stress response, NQO1 was the focus of further investigation. Immunoblotting confirmed the increased expression level of NQO1, and activity assays demonstrated substantial increases in NQO1 activity in SH-SYSY cells after treatment with PDI inhibitors. In summary, this study suggests a novel link between PDI inhibition and NQO1 activity, providing insights into the dynamic interplay between protein folding, oxidative stress, and cell death in neurodegenerative diseases, which can be exploited for drug development in the future.