Background and aim: There are few data on the influence of lupus flare on stroke risk in systemic lupus erythematosus (SLE). In this study, we examined whether a severe lupus flare further increases the risk of stroke among SLE patients. Methods: Using the Taiwan’s National Health Insurance Research Database, we conducted a retrospective population-based cohort study from 2000 to 2016. Each patient with SLE was matched to a non-SLE subject in age, sex, and index date. A severe flare of lupus was identified when an SLE patient was admitted for pulse therapy with intravenous methylprednisolone greater than 250 mg in a single hospitalization. SLE patients were divided into severe flare and non-severe flare groups. Results: In total, 334 of 10,006 patients with SLE had a severe lupus flare, and the remaining 9672 patients were assigned to the non-severe flare group. Ischemic stroke occurred in 29 (8.7%), 485 (5%), and 384 (3.8%) of the patients in the severe flare, non-severe flare, and control groups, respectively. Hemorrhagic stroke occurred in 9 (2.7%), 123 (1.3%), and 37 (0.4%) of patients in the severe flare, non-severe flare, and control groups, respectively. Compared with patients in the non-severe flare group, patients with severe flare had a significantly higher risk of ischemic stroke (adjusted hazard ratio (aHR) = 7.44, 95% confidence interval (CI): 4.93–11.25 vs aHR = 1.52, 95% CI: 1.26–1.83) and hemorrhagic stroke (aHR = 22.49, 95% CI: 10.09–50.12 vs aHR = 4.47, 95% CI: 2.90–6.90). Conclusion: Severe lupus flare is associated with a much higher risk of ischemic and hemorrhagic strokes among SLE patients.