Juvenile idiopathic arthritis (JIA) is a chronic condition known to cause pain-related complications in youth and affect children's physical functioning. There is no data in Arabic children with JIA about the impact of illness upon their physical activity. The objective of this study was to explore physical activity (PA) in children and adolescents with JIA compared with a healthy population and to examine associations between PA, functional ability, and disease activity. Our study included patients with JIA and group control aged between 8 and 17 years. The diagnosis was used according to the International League of Association of Rheumatology (ILAR) criteria 2001. Sociodemographic data and clinical features were collected. Physical activity level and energy expenditure were assessed with a 1-day activity diary and the metabolic equivalent (MET), respectively. Functional ability was assessed with the Moroccan version of the Childhood Health Assessment Questionnaire (CHAQ). Disease activity was measured using the Juvenile Arthritis Disease Activity Score (JADAS). Fifty patients and 50 controls were included (mean ± SD age 11.5 ± 3.3 and 10.5 ± 3.8 years, respectively; p = 0.49) with masculine predominance n = 30 (59.6 %) and n = 29 (58 %), respectively (p = 0.26). The median disease duration was 4.3 years (2-5). The median analog scale (VAS) pain was 20 (10-40). Fourteen patients (28 %) had an active disease. Patient population consisted in majority of oligoarticular arthritis (28 %), 14 patients. The mean of energy expenditure and physical activity were significantly higher in the JIA group. The JIA group spent more time in bed and less time on moderate to vigorous PA than the control group. There is no significant relationship between PA, functional ability, and disease activity. Our study suggests that children and adolescents with JIA have low PA levels and are at risk of losing the benefits of PA. Low PA is not related to functional ability, disease duration, and disease activity in children and adolescent with JIA. A large cohort is necessary to confirm these results.