Multisystem inflammatory syndrome in children (MIS-C) is a pediatric hyperinflammatory syndrome related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection whose epidemiology is not very well known at present. The objective of the study was to better understand the incidence of MIS-C in the Apulia region in southern Italy. Our primary goal was to estimate the incidence of newly identified cases of MIS-C in children aged 0–18 years, during a period of six months, encompassing the second pandemic wave. We also analyzed the characteristics of our cohort in terms of clinical features, treatment, and outcomes. The cumulative incidence of MIS-C was 3.27 per 100,000 residents between 0 and 18 years of age. In our cohort, gastrointestinal, mucocutaneous, and cardiac involvement were the most common clinical features. With our step-up approach to therapy, no patients required intensive care unit (ICU) admission and no cardiac sequelae after 6 months of onset were found in echocardiograms. Conclusion: Our epidemiological study of MIS-C in southern Italy showed unexpectedly overlapping figures with other US studies.