Multisystem inflammatory syndrome in children (MIS-C) secondary to COVID-19 infection in previously healthy children often results in subtle but persistent echocardiographic abnormalities despite complete clinical recovery. This study was done to investigate medium-term cardiovascular outcomes of patients with MIS-C using cardiovascular magnetic resonance imaging (CMR). This is a single-center retrospective study of patients aged less than 21 years, diagnosed with MIS-C who received an outpatient CMR, around 6 months after discharge. CMR was done in patients with significant troponin leak or depressed LVEF. CMR performed on a GE Signa HDxt 1.5 Tesla magnet with a myocarditis protocol. Diagnosis of myocarditis was determined by the original Lake Louise Criteria. There were 21 patients with a median age of 11 years, (IQR 8–13 years), who underwent CMR at median follow-up duration of 6 months (IQR 5–7 months). At the peak of illness during admission, there were 95.2% patients with abnormal Troponin I and BNP. By echocardiogram, 76.2% had left ventricular systolic dysfunction and 9.5% had coronary ectasia, which all resolved by 6 months. By CMR, there were five patients (23.8%) with abnormal left atrial volume, one patient (4.8%) with an abnormal indexed left ventricular end-diastolic volume, and three patients (15%) with abnormal LVEF. There was no evidence of myocardial edema in T2-weighted image sequence. There were three patients with persistent late gadolinium enhancement (14.3%). Follow-up CMR is a useful tool in diagnosing subtle myocardial abnormalities and guide necessity for future follow-up.