Multisystem Inflammatory Syndrome in Children (MIS-C) often involves a post-viral myocarditis and associated left ventricular dysfunction. We aimed to assess myocardial function by strain echocardiography after hospital discharge and to identify risk factors for subacute myocardial dysfunction. We conducted a retrospective single-center study of MIS-C patients admitted between 03/2020 and 03/2021. Global longitudinal strain (GLS), 4-chamber longitudinal strain (4C-LS), mid-ventricular circumferential strain (CS), and left atrial strain (LAS) were measured on echocardiograms performed 3–10 weeks after discharge and compared with controls. Among 60 MIS-C patients, hypotension (65%), ICU admission (57%), and vasopressor support (45%) were common, with no mortality. LVEF was abnormal (< 55%) in 29% during hospitalization but only 4% at follow-up. Follow-up strain abnormalities were prevalent (GLS abnormal in 13%, 4C-LS in 18%, CS in 16%, LAS in 5%). Hypotension, ICU admission, ICU and hospital length of stay, and any LVEF < 55% during hospitalization were factors associated with lower strain at follow-up. Higher peak C-reactive protein (CRP) was associated with hypotension, ICU admission, total ICU days, and with lower follow-up GLS (r = − 0.55; p = 0.01) and CS (r = 0.41; p = 0.02). Peak CRP < 18 mg/dL had negative predictive values of 100% and 88% for normal follow-up GLS and CS, respectively. A subset of MIS-C patients demonstrate subclinical systolic and diastolic function abnormalities at subacute follow-up. Peak CRP during hospitalization may be a useful marker for outpatient cardiac risk stratification. MIS-C patients with hypotension, ICU admission, any LVEF < 55% during hospitalization, or a peak CRP > 18 mg/dL may warrant closer monitoring than those without these risk factors.