Background: Hyperinflammatory response that resembles Kawasaki disease may develop in children after COVID-19 disease, and it is called multisystem inflammatory syndrome in children. The cause of MIS-C is dysregulated innate immune response and a subsequent cytokine storm that results in endothelial damage. It has been determined that low levels of serum 25(OH)D increase the risk of developing immune-related diseases and disorders. Methods: To determine the incidence of hypovitaminosis D, and a possible correlation between 25(OH)D levels and the clinical severity of MIS-C, 21 patients hospitalized in the University Hospital of Split due to MIS-C were evaluated. Results: Hypovitaminosis D was detected in 95% of MIS-C patients. We found a significant relationship between the severity of MIS-C and 25(OH)D levels, as patients with more severe MIS-C had lower 25(OH)D. MIS-C patients with lower vitamin D levels had worse systolic and diastolic function of the left ventricle according to echocardiograms. There was no relationship between 25(OH)D levels and the tested laboratory inflammatory and cardiac markers. Conclusion: Hypovitaminosis D is very common in children with MIS-C and influences the severity of the disease. VD could be a new potential biomarker in MIS-C, and VD replacement therapy should be considered early on in the treatment of MIS-C.