Investigations are still ongoing about the pathophysiology of multi-system inflammatory syndrome in children, which can progress with serious morbidity and mortality after COVID-19 infection. In this study, we aimed to investigate whether fibroblast growth factor-2 and tumour necrosis factor alpha-stimulated gene-6 levels play a role in the diagnosis of the disease and on cardiac involvement. Twenty-three patients (11 girls, 12 boys) and 26 healthy controls (10 girls, 16 boys) were included in the study. The mean age of the patient and control group was 8.45 ± 2.43 and 10.73 ± 4.27 years, respectively. There was no difference between the fibroblast growth factor-2 and tumour necrosis factor alpha-stimulated gene-6 levels of the patient and control groups. When the patients with myocardial involvement in the patient group were compared with the patients without myocardial involvement in terms of fibroblast growth factor-2 and tumour necrosis factor alpha-stimulated gene-6 levels, no difference was found between these groups. The correlation of fibroblast growth factor-2 and tumour necrosis factor alpha-stimulated gene-6 levels with other laboratory parameters was investigated in the patient group. Fibroblast growth factor-2 was moderately inversely correlated with white blood cell count (r = -0.541, p = 0.008), absolute neutrophil count (r = −0.502, p = 0.015) and C-reactive protein (r = −0.528, p = 0.010). Fibroblast growth factor-2 was strongly inversely correlated with erythrocyte sedimentation rate (r = −0.694, p =<0.001). Our data show that fibroblast growth factor-2 and tumour necrosis factor alpha stimulated gene-6 do not provide sufficient information about diagnosis and cardiac involvement in multi-system inflammatory syndrome in children.