Multisystem inflammatory syndrome in children (MIS-C), is a rare but severe, hyperinflammatory complication of COVID-19, in which cardiovascular abnormalities are frequently detected. In this prospective study, we describe the echocardiographic findings in patients with MIS-C, with the use of conventional Echocardiography and Speckle-Tracking Echocardiography (STE) with Left Ventricular (LV) Global Longitudinal Strain (GLS) analysis, in the acute and follow-up phase. In total, 25 MIS-C patients [64% females, mean (± SD) age: 8.3 (± 3.72) years] were included. In the acute phase, median (IQR) Troponin and NT-proBNP and mean heart rate, were 8.07 (14.52) pg/mL, 2875.00 (7713.00) pg/mL, and 102.87 (± 22.96) bpm, respectively. Median (IQR) LV Ejection Fraction (LVEF) was 66 (8)% and LVEF impairment was detected in 2/25 (8%) patients. On follow-up (mean time interval:9.50 ± 4.59 months), heart rate was significantly lower, with a mean value of 90.00 (± 14.56) bpm (p-value = 0.017). Median (IQR) LVEF was 66.00 (6.70)% (p-value = 0.345) and all 25 participants had normal LVEF. In 14/25 patients, additional LV-GLS analysis was performed. During the acute phase, mean LV-GLS was − 18.02 (± 4.40)%. LV-GLS was abnormal in 6/14 patients (42.9%) and among them, only one patient had reduced LVEF. On follow-up (median (IQR) time interval:6.93 (3.66) months), mean LV-GLS was -20.31 (± 1.91)% (p-value = 0.07) and in 1/14 patient (7.1%), the LV-GLS impairment persisted. In conclusion, in the acute and follow-up phase, we detected abnormal LV-GLS values in some patients, in the presence of normal LVEF, indicating that STE-GLS is a valuable tool for identifying subclinical myocardial injury in MIS-C.