Objectives <p>This study compares the prevalence of orofacial signs and symptoms of temporomandibular disorder (TMD) in children with juvenile idiopathic arthritis (JIA) and controls at two study visits two years apart. We also examine the prevalence of TMD diagnoses and their association with general disease activity in children with JIA.</p> Methods <p>In the NorJIA cohort study, children with JIA aged 4 to 16&#xa0;years were recruited consecutively from three pediatric rheumatology clinics in Norway and together with an age- and sex-matched non-JIA control group from public dental health service clinics. Children with JIA were classified into temporomandibular joint (TMJ) involvement and no TMJ involvement groups on the basis of magnetic resonance imaging findings. An adapted version of the Diagnostic Criteria for TMD protocol was applied to assess myalgia, arthralgia, headache attributed to TMD, and disc displacement in all children at both visits.</p> Results <p>Fifty-five children with JIA and TMJ involvement, 132 with JIA without TMJ involvement, and 189 controls completed TMD examinations at both visits. At Visit I, at least one TMD diagnosis was present in 49% of the children with JIA and TMJ involvement, 19% with JIA without TMJ involvement, and 5% of the controls; after two years, these frequencies were 38%, 16%, and 7%, respectively. Children with active JIA disease at baseline had a higher risk of orofacial myalgia (OR 10.5, 95% CI 3.1–36.4).</p> Conclusions <p>TMD was more common in children with JIA than in non-JIA controls. Active JIA disease increased the risk of temporomandibular myalgia, regardless of TMJ involvement. Pediatric rheumatologists and dentists should regularly monitor the orofacial region in all children with JIA.</p> Trial registration <p>Registered retrospectively on clinicaltrials.gov&#xa0;(NCT03904459, 03/04/2019).</p>