Introduction: One of the most prevalent adolescent chronic inflammatory illnesses, juvenile idiopathic arthritis (JIA), is linked to decreased bone mineral density (BMD) and an increased risk of osteopenia and osteoporosis, which raises the risk of fractures. Objective: The aim of the current work was to determine the relationship between disease activity and BMD and bone turnover markers (serum osteocalcin for bone production and C terminal telopeptide of type 1 collagen (CTX) for bone resorption) in patients with juvenile idiopathic arthritis. Materials and Methods: This study included 50 patients with JIA (female: male 20:30). These patients were diagnosed with JIA according to the criteria of classification of the International League of Associations for Rheumatology [ILAR]. BMD was measured by Dual-energy X-ray absorptiometry (DEXA) of the lumbar spine using the Z-score. The results were correlated with juvenile arthritis disease duration, disease activity, serum level of bone turnover markers, and serum level of vitamin D. Clinical disease activity was evaluated by juvenile arthritis disease activity score (JADAS-27). Results: There was a significant negative correlation between BMD (DEXA Z-score) and disease activity (P-value <0.001), bone turnover markers (P-value <0.001), and duration of JIA (P-value <0.05). There was a significant difference between vitamin D level and DEXA Z-score; DEXA Z-score was lower in vitamin D deficient patients. Conclusions: Patients with JIA who have a more active condition are more likely to develop osteopenia and osteoporosis. Osteoporosis incidence may be decreased, and bone health may be improved with timely and effective JIA treatment and disease activity control.