Juvenile Idiopathic Arthritis (JIA) is a paediatric disease of unknown aetiology potentially leading to biomechanical alterations due to local damage of joints. After assessing its reliability, a patient-specific musculoskeletal model of the lower limb was used to investigate the link between joint loading and disease activity in a cohort of JIA children with ankle involvement. We observed a common strategy aiming at protecting the affected ankles with consequent overloading of hip and knee. When quantified at patient specific level, this strategy might allow to identify those cases where a localised steroid injection might not be sufficient to induce remission.