It is reported that alterations in protein glycosylation are present in adult rheumatic diseases; however, the data related to pediatric rheumatic conditions are very scarce. The aim of this study was to assess the effect of juvenile idiopathic arthritis (JIA) on the serum glycosylation profile of transferrin isoforms. Twenty-five patients with different clinical forms of an active JIA and 22 healthy controls were studied. Serum samples were analyzed by capillary electrophoresis on MINICAP electrophoretic system (Sebia, France) to determine the levels of transferrin isoforms. In patients with JIA, tetrasialotransferrin (median 82.6%; range 68.8–99.5) concentration was lower (P = 0.032), and pentasialotransferrin (median 14%; range 0.5–31.2) was higher (P = 0.020) in comparison to controls (median 84.45; range 79.8–87.4; median 11.55; range 9.7–16.1, respectively). No significant correlations between concentration of transferrin isoforms and disease activity score (JADAS 27) or the degree of disability (VAS and CHAQ) were found. Erythrocyte sedimentation rate and CRP levels correlated positively with disialotransferrin (R = 0.493, P = 0.017; R = 0.850, P < 0.001, respectively) and pentasialotransferrin (R = 0.533, P = 0.006; R = 0.491, P = 0.045, respectively), and negatively with trisialotransferrin (R = − 0.546, P = 0.007; R = − 0.515, P = 0.049, respectively) and tetrasialotransferrin (R = − 0.436, P = 0.029; R = − 0.504, P = 0.039, respectively). This preliminary study shows the shifts in transferrin isoforms profile among patients with JIA. Our data indicate a potential clinical utility of the transferrin isoforms measurement, especially tetrasialotransferrin and pentasialotransferrin. Further prospective studies on larger groups of patients should be conducted to validate the results.