Objective <p>This study aims to investigate the causal relationship among gut microbiota, ferroptosis-related genes, and Kawasaki disease, as well as the potential mediating effects involved.</p> Methods <p>A bidirectional two-step two-sample Mendelian randomization (MR) approach was employed, utilizing genome-wide association study (GWAS) data from publicly available databases, covering 473 gut microbiota taxa, ferroptosis-related genes, and Kawasaki disease. The first step analyzed the causal relationships between ferroptosis-related genes and Kawasaki disease, as well as between gut microbiota and Kawasaki disease. The second step assessed the causal associations between significant gut microbiota taxa and ferroptosis-related genes, followed by a mediation analysis. Sensitivity and heterogeneity analyses were conducted to evaluate the robustness of the results.</p> Results <p>In the first step, seven ferroptosis-related genes were identified as significantly influencing the occurrence of Kawasaki disease. Among them, MDM4, FABP4, PARK7, RARRES2, and TF were protective genes, while HMOX1 and NQO1 were risk genes. Additionally, 19 gut microbiota taxa showed significant causal relationships with Kawasaki disease, with Fusobacteriaceae exhibiting the strongest protective effect and UBA11963 showing the highest risk effect. In the second step, seven significant gut microbiota–ferroptosis gene associations were identified. Mediation analysis revealed that CAG-269 sp002372935 promoted Kawasaki disease occurrence by downregulating FABP4 expression, with a mediation effect of 0.197 and a mediation proportion of 20.76%.</p> Conclusion <p>This study suggests that gut microbiota may influence Kawasaki disease by regulating the expression of ferroptosis-related genes, providing novel genetic evidence for the disease’s pathogenesis. Furthermore, gut microbiota and ferroptosis-related genes may serve as potential targets for Kawasaki disease prevention and treatment.</p>