Background and Purpose: The Gram-negative bacterium lipopolysaccharide (LPS) is frequently administered to generate models of systemic inflammation. In particular, both kidney and lung are more sensitive to acute injury caused by LPS-induced systemic inflammation. However, there are several side effects and no effective treatment for LPS-induced systemic inflammation. Experimental approach: The PEGylated PDZ peptide was synthesized based on the PDZ motif of ZO-1 protein. We investigated the anti-inflammatory effect of PEGylated PDZ peptide on LPS-induced systemic inflammation in mice. We also performed the RNA-Sequencing analysis to know the expression pattern of 24,424 genes according to each comparison combination. Key Results: PDZ peptide administration led to restoration of tissue injuries (kidney, liver, and lung) and prevented alterations in biochemical plasma markers. The production of pro-inflammatory cytokines was significantly decreased in the plasma and lung BALF in the PDZ-administered mice. Flow cytometry analysis revealed the PDZ peptide significantly inhibited inflammation, mainly by decreasing the population of M1 macrophages, neutrophils, and increasing M2 macrophages. Using RNA sequencing analysis, the expression levels of the NF-κB-related proteins were lower in PDZ-treated cells than in LPS-treated cells. Wild-type PDZ peptide significantly increased mitochondrial membrane integrity and decreased LPS-induced mitochondria fission. PDZ peptide dramatically could reduce LPS-induced NF-κB signaling, ROS production, and the expression of M1 macrophage marker proteins, but increased the expression of M2 macrophage marker proteins. Conclusion and Implication: These results indicated PEGylated PDZ peptide inhibits LPS-induced systemic inflammation, reducing tissue injuries and reestablishing homeostasis and may be a therapeutic candidate against systemic inflammation.