Background Multisystem inflammatory syndrome in children (MIS‐c) is associated with severe cardiovascular impairment and eventually death. Pathophysiological mechanisms involved in myocardial injury were scarcely investigated, and cardiovascular outcomes are uncertain. Autopsy studies suggested that microvascular dysfunction may be relevant to LV impairment. Objective We aimed to evaluate segmental LV longitudinal strain by 2DST echocardiography and myocardial flow reserve (MFR) by 13 N‐ammonia PET‐CT, in six surviving MIS‐c patients. Methods Each patient generated 34 LV segments for combined 2DST and MRF analysis. MFR was considered abnormal when <2, borderline when between 2 and 2.5 and normal when >2.5. Results From July 2020 to February 2021, six patients were admitted with MIS‐c: three males, aged 9.3 (6.6–15.7) years. Time from admission to the follow‐up visit was 6.05 (2–10.3) months. Although all patients were asymptomatic and LV EF was ≥55%, 43/102 (42.1%) LV segments showed MFR <2.5. There was a modest positive correlation between segmental peak systolic longitudinal strain and MFR: r = .36, p = .03 for basal segments; r = .41, p = .022 for mid segments; r = .42, p = .021 for apical segments. Median peak systolic longitudinal strain was different among MRF categories: 18% (12%–24%) for abnormal, 18.5% (11%–35%) for borderline, and 21% (12%–32%) for normal MFR (p = .006). Conclusion We provided preliminary evidence that surviving MIS‐c patients may present subclinical impairment of myocardial microcirculation. Segmental cardiac strain assessment 2DST seems useful for MIS‐c cardiovascular follow‐up, given its good correlation with 13 N‐ammonia PET‐CT derived MFR.