In this study, the relation between the nitric oxide (NO) levels in the serum and fraction of exhaled nitric oxide (FENO) in children with juvenile idiopathic arthritis (JIA) and the activation criteria of the disease has been investigated. The study group consisted of 35 JIA-diagnosed patients and 18 healthy children. According to the clinical and laboratory findings, the patients with JIA were divided into two groups, active (group I) and in remission (group II). The healthy children were classified as group III. The activation criteria of the disease were determined for each patient. The serum NO level and FENO level were measured in all the patients. In the group with JIA, correlation was detected between FENO level and number of involved joints and number of joints with limited motion. In addition, correlation was determined between the FENO level and number of involved joints in group I and the serum NO level and activity score in group II. However, it was seen that there is no statistical difference in the serum NO level and FENO level of the patients with JIA and the control group and groups I and II. This study demonstrated the correlation between FENO level and number of involved joints and number of joints with limited motion in patients with JIA. Our results matter in terms of FENO being a noninvasive laboratory marker in following the progression of the disease.