<b><i>Background:</i></b> No epidemiologic study has previously reported on the associations among Behçet’s disease (BD) and autoimmune disorders. <b><i>Objectives:</i></b> To investigate the association between BD and the autoimmune disorders multiple sclerosis and rheumatoid arthritis. <b><i>Methods:</i></b> Medical records of patients newly diagnosed with BD (<i>n</i> = 6,214) in 2012–2017 were analyzed using data entered into a large, nationwide database from 2007 to 2017. An age- and sex-matched control population of individuals without BD was sampled at a ratio of controls:BD cases of 3:1 (<i>n</i> = 18,642). Both cohorts were analyzed for the presence of multiple sclerosis or rheumatoid arthritis within a minimum of 5 years prior to their BD diagnosis. <b><i>Results:</i></b> Patients with BD had significantly higher odds ratios (ORs) for multiple sclerosis (8.85 [95% CI 2.36–33.17]) and rheumatoid arthritis (4.62 [95% CI 3.35–6.35]) than the control group after adjustment for diabetes mellitus, hypertension, and dyslipidemia. BD patients aged <40 years had a higher proportion of rheumatoid arthritis (OR 23.91, 95% CI 5.50–103.9) than older patients (OR 3.96, 95% CI 2.83–5.54). <b><i>Conclusion:</i></b> Our results suggest that BD is associated with multiple sclerosis and rheumatoid arthritis.