This study aims to evaluate the body composition (BC) of female children and adolescents with juvenile idiopathic arthritis (JIA). A cross-sectional, controlled study was performed to compare the BC between 42 JIA girls and 35 healthy controls, matched for age and gender. Weight and height were used to calculate body mass index (BMI), classified as a Z-score (Z-BMI). BC was evaluated by dual-energy X-ray absorptiometry (DXA; DPX-L, Lunar). The fat mass index (FMI) was calculated as the ratio between total fat mass and height squared (kilograms per square metre). The lean mass index (LMI) was calculated as the ratio between total lean mass and height squared (kilograms per square metre). In JIA patients, the median of age was 13 years (6-19) and median disease duration was 84 months (10.0-215.0). The main disease subtype was polyarticular arthritis (54.8%). We observed that 61.9% of patients had normal Z-BMI. JIA girls had higher median Z-BMI scores (0.17 vs. -0.48, p = 0.034), total body fat percentages (26.5% vs. 16.4%, p = 0.001), truncal fat (4.52 vs. 2.32, p = 0.011) and FMI (4.83 vs. 2.23, p < 0.001). For LMI, there was no difference between JIA girls and controls (13.45 vs. 12.45, p = 0.212). We did not find association between FMI and age, disease subtype, number of limited and/or active joints, months since diagnosis and use of corticosteroids or methotrexate. BC changes found in JIA girls, such as fatness and adiposity, indicate a potentially greater risk for developing hypertension, diabetes mellitus and cardiovascular diseases. These findings emphasise the importance of evaluating nutritional status and body composition to minimise the emergence of chronic diseases later in life.