We investigated the association between autoimmune thyroid disease and systemic lupus erythematosus (SLE) using nationwide insurance claims data for the entire Korean population. Claims data for the period 2009-2013 were retrieved from the National Health Insurance System database. SLE and thyroid disease were identified using the International Classification of Diseases codes and medication information. Logistic regression analyses were used to evaluate the association between SLE and thyroid disease. The study used records from 17,495 patients with SLE and 52,485 age- and sex-matched control subjects. A greater prevalence of Graves' disease (0.94% vs. 0.46%, P < 0.001), Hashimoto's thyroiditis (2.68% vs. 0.80%, P < 0.001), and thyroid cancer (1.81% vs. 1.30%, P < 0.001) was observed in SLE patients than in control subjects. Multivariate regression analyses demonstrated that SLE was significantly associated with an increased risk of both autoimmune thyroid disease and thyroid cancer (Graves' disease: odds ratio [OR] 2.07, 95% confidence interval [CI] 1.70-2.53; Hashimoto's thyroiditis: OR 3.42, 95% CI 3.00-3.91; thyroid cancer: OR 1.40, 95% CI 1.22-1.60). Age- and sex- stratified analyses revealed that the risk of autoimmune thyroid disease in SLE patients was increased for all age groups and the female group. An association between thyroid cancer and SLE was identified only in the 20- to 59-year-old age group and in the female group. Using a large population-based study, we demonstrated that patients with SLE are at a greater risk of developing thyroid disease than matched control individuals.