Objective: To identify factors associated with the higher proportion of fatty tissue and overweight/obesity observed in patients with juvenile idiopathic arthritis (JIA). Patients and methods: We performed a cross-sectional study of 80 JIA patients aged 4–15 years with 80 age- and sex-matched healthy controls. Body composition was assessed using dual-energy x-ray absorptiometry. The 27-joint Juvenile Arthritis Disease Activity score (JADAS27) was calculated. Two multivariate models were constructed to identify factors associated with overweight/obesity and fat mass index (FMI). Results: No differences were found between cases and controls in body mass index (BMI) or body composition. However, compared with controls, patients with a high inflammatory activity (JADAS27 > 4.2 for oligoarticular JIA or >8.5 for polyarticular disease) had higher values for BMI (p = 0.006); total fat mass (p = 0.003); FMI (p = 0.001); and fat in the legs (p = 0.001), trunk (p = 0.001), and arms (p = 0.002). The factors associated with overweight/obesity in patients were the duration of therapy with biological drugs, measured in months (OR 95% CI = 1.12 1.02–1.04; p = 0.037), and physical activity (OR 95% CI = 0.214 0.07–0.68; p = 0.010), while the factors associated with FMI were age (β 95% CI = 0.30 0.17–1.41; p = 0.014), JADAS27 (β 95% CI = 0.45 0.16–1.08; p = 0.009), and physical activity (β 95% CI = −0.22 −5.76 to 0.29; p = 0.031). Conclusion: Our study revealed no differences between JIA patients with well-controlled disease and low disability and the healthy population in BMI or body composition. Furthermore, the association observed between inflammatory activity and adiposity could be responsible for poorer clinical course.