We evaluated the incidence of temporomandibular disorder (TMD) in patients with rheumatoid arthritis (RA) and examined the association between TMD and RA, through longitudinal follow-up. Population data from the Korean National Health Insurance Service-Health Screening Cohort from 2002 to 2015 was used. From 514,866 subjects, 3122 with RA were matched with 12,488 controls in a 1:4 ratio. The crude and adjusted models (for obesity, smoking, alcohol consumption, blood pressure, blood glucose, total cholesterol, and Charlson Comorbidity Index scores) were calculated. Chi-square tests, Kaplan-Meier (KM) analysis, and two-tailed analyses were used for statistical analysis. Stratified Cox proportional hazard models were used to assess the hazard ratios (HR) and 95% confidence intervals (CI) for TMD in the RA group, compared to those in the control group. The adjusted HR for TMD in RA was 2.52 (95% CI = 1.70–3.74), compared to the control group. The results were consistent with the subgroup analyses, according to age and sex, except in men older than 60 years of age. KM analysis showed similar results. Hence, we found that patients with RA have a higher risk of TMD, and should be observed for symptoms of the initial stage of TMD to prevent the risk of aggravation.