Background The comparative risk of cause-specific mortality in patients with Behçet disease (BD) vs. the general population is not known. Objectives To compare the risk of all-cause and cause-specific mortality in patients with BD vs. the general population. Methods Using data from the Korea National Health Insurance Service database for the period 2002–20, we conducted a cohort study comparing patients with BD with the general population, matched according to age and sex (1: 4 ratio). We used Cox proportional hazard models to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for all-cause and cause-specific mortality. Subgroup analyses by age and sex were done. Results We included 24 669 patients with BD and 98 676 age- and sex-matched controls [mean (SD) age 40.5 (12.9) years; 34% male]. During a mean follow-up of 11.9 years, the incidence rate (IR) of death per 100 person-years was 0.36 in patients with BD and 0.29 in controls [hazard ratio (HR) 1.28, 95% confidence interval (CI) 1.20–1.38]. The risk of mortality was highest in the first year after BD diagnosis (HR 2.66, 95% CI 2.09–3.40). Patients with BD died more often in this period as a result of malignancy (HR 1.96, 95% CI 1.30–2.98); cardiovascular (HR 2.68, 95% CI 1.45–4.97), gastrointestinal (HR 3.50, 95% CI 1.35–9.07) and respiratory disease (HR 5.00, 95% CI 1.34–18.62); and infection (HR 3.33, 95% CI 1.02–10.92). Mortality as a result of neurological (HR 1.58, 95% CI 1.06–2.35) or genitourinary disease (HR 2.20, 95% CI 1.43–3.37) was also more common in patients with BD during the overall follow-up. Subgroup analyses showed consistent results. The risk of cardiovascular mortality vs. the general population was higher in younger patients (P=0.006) and the risk of gastrointestinal mortality was increased in women vs. men (P=0.04). Conclusions This population-based cohort study revealed that the first year after diagnosis is the highest risk period for excess mortality in people with BD. The mortality burden in BD derives from a wide spectrum of organ involvement and should serve as a warning to clinicians about the systemic nature of the disease.