Background: Multisystem inflammatory syndrome in children is a new, rare, post-infectious complication of SARS-CoV-2 infection in children. The aim of this study was to display the role of therapeutic plasma exchange on cardiovascular outcomes in children with multisystem inflammatory syndrome. Methods: This study included children who met the diagnostic criteria for multisystem inflammatory syndrome and who were admitted to the intensive care unit. This is a prospective single-center study conducted between August 2020 and September 2021. Subjects had cardiac involvement which was defined as elevated troponin I, abnormal electrocardiographic and echocardiographic findings. Patients were followed by a pediatric cardiologist throughout the intensive care unit stay and after discharge for 12 months. Patients were divided into two groups which received therapeutic plasma exchange and which did not. Results: 38 children were included in this study. There were 16 patients in the no plasma exchange group and 22 patients in the plasma exchange group. The two groups were similar in age, sex, leucocyte, thrombocyte count, neutrophil percentage, hemoglobin, C-reactive protein, erythrocyte sedimentation rate, alanine aminotransferase, albumin, ferritin, fibrinogen, D-dimer, IL-6, troponin I, number of electrocardiographic abnormalities and patients with mitral valve regurgitation detected at admission (p > 0.05). There was no significant difference between the two groups in terms of duration of normalization of electrocardiographic abnormalities and disappearance of mitral valve regurgitation (p > 0.05). Duration of normalization of troponin I (2, IQR 1–4, versus 5, IQR 3–9 days; p = 0.044) and length of hospital stay (7, IQR 6–10, versus 13, 8–20 days; p = 0.001) was longer in the plasma exchange group. Conclusions: We did not observe any significant improvement in children having undergone plasma exchange as compared to children who did not. On the opposite, their length of hospital stay and time to troponin I normalisation were even longer. Some baseline differences in cardiac attainment severity may partly explain this finding.