Multilayer strain magnetic resonance imaging (MRI) analysis offers detailed insights into myocardial mechanics and cardiac function by assessing different layers of the heart muscle, enabling a comprehensive understanding of cardiac involvement. This study aims to explore cardiac strain differences between patients with multisystem inflammatory syndrome and a control group at medium-term follow-up, utilizing a layer-specific cardiac magnetic resonance imaging (CMR) approach. In this retrospective study, patients with multisystem inflammatory syndrome in children (MIS-C) and a group of controls who had undergone cardiac magnetic resonance (CMR) imaging were selected and included. CMR was performed 30days after discharge (range 34-341days) for MIS-C patients. TrufiStrain research prototype software (Siemens Healthineers AG, Erlangen, Germany) was used for automated myocardial segmentation and strain calculation, to measure radial strain (RS), circumferential strain (CS), and longitudinal strain (LS) at the epicardial, mid-wall, and endocardial levels. Statistical analysis included Shapiro-Wilk tests, Student t-tests, and Mann-Whitney U tests, ANOVA, and regression analysis, maintaining a significance level of α = 0.05. The study cohort consisted of 32 MIS-C patients (≤ 18years; 14 females) and 64 control participants (≤ 18years; 24 females). Median interval to CMR post diagnosis was 142days (range 34-341) with normal CMR findings for all patients. The mean age of the two groups was similar (MIS-C: 14.2years; controls: 14.1years, P = 0.49). There were no significant differences in height (MIS-C: 164.7cm; controls: 163.9cm, P = 0.84), weight (MIS-C: 68.2kg; controls: 59.4kg, P = 0.11), or body surface area (MIS-C: 1.7 m2; controls: 1.7 m2, P = 0.41). Global strain measurements showed no significant differences between the groups (global LS MIS-C patients - 16.2% vs - 15.7% in controls (P = 0.23); global RS 27.8% in MIS-C patients vs 29.5% in controls (P = 0.35); and global CS - 16.7% in MIS-C patients vs - 16.8% in controls (P = 0.92)). Similarly, layer-specific strain analysis across the endocardial (LS values of - 17.7% vs - 16.8% (P = 0.19), RS of 23.1% vs 24.8% (P = 0.25), and CS of - 19.9% vs - 19.9% (P = 0.92)), epicardial (LS - 14.9% vs - 14.5% (P = 0.31), RS of 31.2% vs 33.1% (P = 0.29), and CS of - 14.1% vs - 14.2% (P = 0.75)), and midmyocardial (LS - 16.5% vs - 16.3% (P = 0.18), RS 29.3% vs 31.8% (P = 0.31), and CS - 17.0% vs - 17.2% (P = 0.95)) levels revealed no significant disparities. The only notable finding was the reduced apical radial strain in MIS-C patients compared to controls (global RS MIS-C 12.4% vs 17.4% in controls, P = 0.03; endocardium RS MIS-C 4.9% vs 10.31% in controls, P = 0.01; epicardial RS MIS-C 17.7% vs 22.6% in controls, P = 0.02; and midmyocardium RS MIS-C 12.5% vs 17.9% in controls, P = 0.02). This study demonstrates that MIS-C does not significantly impact global or layer-specific myocardial strain values, as assessed by CMR, compared to a control group. The lower apical radial strain in MIS-C patients indicates a potential localized myocardial involvement.