<b><i>Background:</i></b> Up to 25% of patients with cutaneous lupus erythematosus (CLE) can develop systemic lupus erythematosus (SLE). However, the risk of autoimmune diseases other than SLE in CLE patients who have only skin manifestations (CLE-alone) has rarely been explored. <b><i>Objective:</i></b> To investigate the long-term risk and independent factors of non-SLE autoimmune diseases among CLE-alone patients. <b><i>Method:</i></b> A nationwide cohort study using the Taiwanese National Health Insurance Research Database 1997–2013. CLE patients and matched subjects were included. Cumulative incidences of autoimmune diseases after 1 year of CLE-alone diagnosis were compared. Cox proportional hazard model was also performed. <b><i>Results:</i></b> A total of 971 CLE-alone patients and 5,175 reference subjects were identified. The 10-year cumulative incidence of autoimmune diseases other than SLE was significantly elevated in the CLE-alone cohort (9.00%, 95% confidence interval [CI] 6.72–11.29) than in the reference cohort (4.20%, 95% CI 3.53–4.87%) (<i>p</i> < 0.001). CLE-alone was independently associated with non-SLE autoimmune diseases (adjusted hazard ratio 1.55, 95% CI 1.10–2.18). Among CLE-alone patients, females and those taking long-term systemic corticosteroids (a proxy for extensive disease) were associated with non-SLE autoimmune diseases after adjusting for the number of repeated autoimmune laboratory tests. <b><i>Conclusion:</i></b> CLE-alone is independently associated with future non-SLE autoimmune diseases.