Multisystem Inflammatory Syndrome in Children (MIS-C) is a known severe condition affecting children previously exposed to SARS-CoV-2. The aim of our study was to describe the early cardiac abnormalities in patients with MIS-C, evaluated by speckle tracking echocardiography (STE) and cardiac MRI (CMR). Clinical, laboratory and microbiological data were measured for all patients. All children underwent standard transthoracic echocardiography, STE with analysis of left ventricle global longitudinal strain (GLS). Seventeen (75%) of the children were evaluated with CMR. Twenty-three patients (13M, 10F) were recruited, mean age was 8.1 ± 4 years. Cardiovascular symptoms were present in 10 (43.5%). Nine children (39.1%) shared Kawasaki Disease-like symptoms. Four patients (17.4%) needed ICU admission. In-hospital survival was 100%. TnI was elevated in 15 (65.2%) and BNP in 20 (86.9%) patients. The median time to STE evaluation was 8 days and to CMR was 18 days after fever onset. Mean LVEF was 59 ± 10%. Coronary dilation was observed in six (26.1%) patients. STE showed a reduced mean LVGLS (−17 ± 4.3%). LGE with a non-ischemic pattern was evident in six out of seventeen patients (35.2%). The elevation of myocardial necrosis markers, the reduction of LVGLS and the presence of LGE on CMR in about a quarter of MIS-C patients supports the hypothesis of a post-viral immune-mediated myocarditis-like pathogenesis.