Our study aimed to evaluate the clinical and laboratory features of juvenile idiopathic arthritis (JIA) children with temporomandibular joint (TMJ) arthritis. In the retrospective cohort study, we analyzed data of 753 patients with JIA aged 2–17 years, depending on TMJ arthritis or not. TMJ arthritis can to be diagnosed in the presence of at least two of the following clinical signs of inflammation: pain in TMJ, jaw opening limitation, jaw opening deviation, and micrognathia. We compared clinical, laboratory, and treatment features in JIA patients depending on the involvement of TMJ. TMJ arthritis was detected in 43 (5.7%) of our patients and associated with a longer course of the disease, polyarticular JIA category, treatment with systemic corticosteroids, and longer achievement of the remission and involvement of cervical spine, hip, and shoulder. Active joints >8 (OR = 14.9,p= 0.0000001), delayed remission >7 years (OR = 3.1;p= 0.0004), delayed hip involvement (OR = 4.6;p= 0.041), hip osteoarthritis (OR = 4.0;p= 0.014), cervical spine arthritis (OR = 10.3,p= 0.000001), and corticosteroid treatment (OR = 2.3,p= 0.0007) were associated with TMJ involvement. Patients with TMJ arthritis require more biologics (OR = 3.2,p= 0.0006, HR = 2.4,p= 0.005) and have decreased probability of remission achievement (p= 0.014). Consequently, TMJ arthritis was associated with a severe disease course. Early biologic treatment and corticosteroid avoidance might decrease TMJ involvement.