Background Temporomandibular joint (TMJ) arthritis is common in children with juvenile idiopathic arthritis (JIA), but often clinically asymptomatic. Magnetic resonance imaging (MRI) is the most reliable examination method, but requires sedation in young children. The aim of our study was to evaluate whether early TMJ MRI will change the treatment of patients with newly diagnosed JIA. Methods Single center chart review of all patients with a diagnosis of JIA between January 2007 and December 2010. Results We found 147 patients with newly diagnosed JIA during this period. In 111 (76%) at least 1 MRI of the TMJ was available. Reasons why no TMJ MRI was done were parents’ refusal (10), MRI of other locations (7), fixed dental appliances (16) and unclear cause (3). A diagnosis of TMJ arthritis based on increased joint enhancement on MRI was made in 91/111 (82%) patients. The first MRI was done at a median interval of 5 months from the diagnosis of JIA, and 61/111 patients (55%) required sedation for their first MRI. TMJ arthritis was diagnosed in 53/61 (87%) requiring sedation and in 34/50 (68%) patients without sedation (p = 0.003). Following the first TMJ MRI, intra-articular steroid injections were performed into 107 TMJs of 60 patients. 48/147 (33%) patients received at least one DMARD to control their disease, and in 9/48 (19%) the first DMARD was started following the first TMJ MRI. Factors associated with TMJ involvement as demonstrated by MRI were JIA subtype (p = 0.007) and a younger age at diagnosis of JIA (p = 0.04). Conclusion In our cohort of newly diagnosed JIA patients TMJ arthritis was very common. Early TMJ MRI led to changes in treatment in 62% of patients with additional joint injections in 60 patients and start of systemic medication in 9 patients. We especially recommend performing TMJ MRI in young children even if they require sedation, as they have an increased rate of TMJ involvement.