Background: Kawasaki disease (KD) is a common multi-system vascular inflammatory disease in childhood. The main complication is coronary artery lesions (CALs). Despite its widespread prevalence, the precise pathogenesis of KD remains unknown. The purpose of this study is to investigate the potential therapeutic role and mechanism of Oridonin (Ori) in improving vascular endothelial cell injury in KD. Methods: The synthetic biotin coupled with Ori pulls down lysate protein products from Human umbilical vein endothelial cells (HUVECs). Subsequently, the pull-down proteins were detected using Liquid Chromatography-tandem Mass Spectrometry (LC-MS/MS), and bioinformatics analysis was utilized to screen for the key Ori binding protein Peptidylarginine Deiminase 2 (PADI2). HUVECs were then pretreated with various concentrations of Ori, including 0.5 μM, 1.0 μM, and 2.0 μM. The monocytic leukemia cell line (THP1) was treated with 15% serum obtained from KD patients and co-cultured with HUVECs to reconstruct the inflammatory environment of endothelial cells in KD. Moreover, by constructing the PADI2 interference plasmid for cell regulation experiments and in vivo experiments on mice injected with lactobacillus casei cell wall extract (LCWE) solution, the underlying mechanism of Ori treatment against KD was determined using Cell Counting Kit-8 (CCK-8), flow cytometry, Enzyme-Linked Immunosorbent Assay (ELISA), quantitative Real-Time Polymerase Chain Reaction (qRT-PCR), and Western blot techniques. Results: The key Ori binding protein PADI2 was screened using LC-MS/MS detection of Ori pull-down proteins. Ori therapy improves KD-induced endothelial cell inflammatory damage, as evidenced by increased cell viability, reduced apoptosis, and decreased levels of pro-inflammatory cytokines like Interleukin-1β (IL-1β), Interleukin-6 (IL-6), and Tumor necrosis factor-α (TNF-α) (p < 0.05). Additionally, Ori greatly reduced the expression of PADI2, phosphorylated NF-kappaB p65 (p-p65), and phosphorylated inhibitor of nuclear factor-kappa B (NF-κB) (phosphorylated inhibitor of NF-κB (p-IκB)) in HUVECs (p < 0.05). Ori demonstrated the optimum efficiency at 2 μM concentration (p < 0.05). Interfering with PADI2 markedly increased KD-induced HUVEC cell viability and inhibited apoptosis (p < 0.01). This interference also reduced the levels of IL-1β, TNF-α, and IL-6 along with downregulating the expression of PADI2, p-p65, and p-IκB (p < 0.01). The results of in vivo experiments revealed that both Ori and interfering with PADI2 alleviated coronary endothelial cell injury and inflammation. They also significantly elevated Nitric Oxide (NO) levels (p < 0.01), and significantly reduced endothelin (ET)-1 and pro-inflammatory cytokine levels (p < 0.01), as well as the expression of p-p65 and p-IκB in coronary tissue of mice (p < 0.01). Interference with PADI2 based on Ori stimulation significantly reduced p-p65 and p-IκB expression (p < 0.01). Conclusions: Ori exhibited the ability to improve the inflammatory damage of endothelial cells in KD by regulating the expression and viability of PADI2 to affect the activation of the NF-κB pathway and nuclear transport.