Objective A relatively common occurrence of spontaneous subarachnoid hemorrhage (SAH) in patients with systemic lupus erythematosus (SLE) has been noted; however, the subsequent studies were conflicting. This nationwide population-based study aimed to evaluate the risk of SAH in patients with SLE. Methods We identified 16,967 SLE patients from the Taiwan National Health Insurance (NHI) database between 2000 and 2006, and compared the incidence rate of SAH with 16,967 randomly selected age- and sex-matched non-SLE subjects. A Cox multivariable proportional hazards model was used to evaluate the risk factors of SAH in the SLE cohort. Results The SLE cohort had a higher risk of SAH, with an incidence rate ratio of 4.84 (P < 0.001). Despite a younger age, the mortality rate after SAH was significantly higher in the SLE cohort compared to all of the non-SLE SAH patients identified from the 1 million NHI beneficiaries (60.0% versus 38.9%; P = 0.007). Age (hazard ratio [HR] 1.03, 95% confidence interval [95% CI] 1.01-1.05), platelet transfusion (HR 2.75, 95% CI 1.46-5.17), red blood cell transfusion (HR 7.11, 95% CI 2.81-17.97), and a mean daily steroid dose >10 mg of prednisolone or equivalent (HR 4.36, 95% CI 2.19-8.68) were independent risk factors for the new onset of SAH. Conclusion This study demonstrated that SAH is a rare but associated complication of SLE with a high mortality rate. Other than age, higher mean daily steroid use and a history of platelet or red blood cell transfusion were associated with the occurrence of SAH in patients with SLE.