Non-resolving inflammation mediated by monocytes and macrophages is known to be involved in the pathogenesis of atherosclerosis. However, the role and regulation of neutrophils during the establishment of sustained inflammation and atherosclerosis are less well understood. We observed that chronic subclinical endotoxemia, a risk factor for non-resolving low-grade inflammation, significantly exacerbated atherosclerosis in high-fat-diet (HFD) fed ApoE deficient mice accompanied by the polarization of neutrophils into a pro-inflammatory phenotype. Neutrophils primed with super low dose LPS in vitro demonstrated a similar phenotype, as reflected in elevated levels of inflammatory mediators (CD11b, Dectin-1, MMP9 and LTB4) and reduced levels of homeostatic mediators (LRRC32 and FPN). The polarization of non-resolving inflammatory neutrophils was potentially due to the disrupted peroxisome homeostasis and compromised peroxisome-lysosome fusion, which induced intracellular ROS accumulation and subsequent up-regulation of oxCAMKII and 5-LOX. Application of 4-phenylbutyrate (4-PBA), which enhanced peroxisome homeostasis of neutrophils, not only reduced oxCAMKII and 5-LOX levels, but also re-balanced the expression profiles of pro- and anti-inflammatory mediators. 4-PBA treatment potently restored LPS induced neutrophil polarization. Through transfusing differentially programmed neutrophils into HFD fed mice, we directly examined the outcomes of re-programmed neutrophils during the pathogenesis of atherosclerosis. Adoptive transfer of neutrophils primed with subclinical LPS resulted in elevated atherosclerotic plaque size, increased lipid deposition as well as diminished plaque collagen content. In contrast, the mice receiving neutrophils programmed with 4-PBA exhibited suppressed atherosclerosis development and strengthened plaque stability as compared to the mice that were transferred with PBS treated neutrophils. Taken together, our data have defined novel neutrophil dynamics responsible for controlling non-resolving inflammation versus resolving homeostasis during atherosclerosis, and also provided the feasibility of employing re-programmed neutrophils to treat atherosclerosis.