Nicotinamide adenine dinucleotide phosphate (NADPH) oxidases (NOX) involvement has been established in the oncogenic cell signaling of acute myeloid leukemia (AML) cells and in the crosstalk with their niche. We have shown an expression of NOX subunits in AML cell lines while NOX activity is lacking in the absence of exogenous stimulation. Here, we used AML cell lines as models to investigate the specificity of VAS3947, a current NOX inhibitor. Results demonstrated that VAS3947 induces apoptosis in AML cells independently of its anti-NOX activity. High-performance liquid chromatography (HPLC) and mass spectrometry analyses revealed that VAS3947 thiol alkylates cysteine residues of glutathione (GSH), while also interacting with proteins. Remarkably, VAS3947 decreased detectable GSH in the MV-4-11 cell line, thereby suggesting possible oxidative stress induction. However, a decrease in both cytoplasmic and mitochondrial reactive oxygen species (ROS) levels was observed by flow cytometry without disturbance of mitochondrial mass and membrane potential. Thus, assuming the consequences of VAS3947 treatment on protein structure, we examined its impact on endoplasmic reticulum (ER) stress. An acute unfolded protein response (UPR) was triggered shortly after VAS3947 exposure, through the activation of inositol-requiring enzyme 1α (IRE1α) and PKR-like endoplasmic reticulum kinase (PERK) pathways. Overall, VAS3947 induces apoptosis independently of anti-NOX activity, via UPR activation, mainly due to aggregation and misfolding of proteins.