Data on Kawasaki disease from tropical countries are scarce. Hence, this population-based study aims to determine the epidemiology, clinical characteristics, and outcome of Kawasaki disease in children enrolled in the Kawasaki disease registry between 2006 and 2019 in Southern Malaysia. Diagnosis of Kawasaki disease was made using standard criteria. Primary outcome measure was a coronary artery aneurysm. Multivariable logistic regression was used to analyze the associated risk factors for coronary artery aneurysm. There were 661 Kawasaki disease, with 27% incomplete and 11% atypical presentations. Male-to-female ratio was 2:1, and median age of diagnosis was 1.4 years (interquartile range 9 to 32 months). Incidence in children of less than 5 years was 14.8 (95% confidence interval [CI]: 13.6 to 16.0) per 100,000 population, higher in males (19/100,000) and Chinese (22/100,000), with a gradual increase from 5.7/100,000 in 2006 to 19.6/100,000 in 2019, p < 0.001. Incidence in children between 5 and 9 years old was 1.3 (95% CI: 0.9 to 1.6) per 100,000 population and remained stable over time. There was a seasonal pattern with peak incidence during the rainy season. Out of 625 intravenous immunoglobulins (IVIG)-treated Kawasaki disease, 7.4% were resistant, and 9% had coronary artery aneurysms. Atypical presentation, male sex, late diagnosis, and IVIG resistance were independent risk factors for coronary artery aneurysms.Conclusions: Despite the tropical climate, Kawasaki disease epidemiology is similar to non-tropic regions with seasonal patterns and a rising incidence. Atypical presentation, male sex, late diagnosis, and IVIG resistance were significantly associated with coronary artery aneurysms. What is Known: • Kawasaki disease predominantly occurs in males, children less than 5 years old, and the Asian population. • Male sex, late diagnosis, incomplete Kawasaki disease, and IVIG resistance were associated with coronary artery aneurysms. What is New: • In multi-ethnic Asian countries such as Malaysia, ethnic Chinese have a higher prevalence of Kawasaki disease compared to other ethnicities. • Kawasaki disease with atypical presentation can occur in both complete and incomplete Kawasaki disease and is significantly associated with a coronary artery aneurysm.