Introduction Previous studies have suggested that both bipolar disorder and atopy are associated with an increased risk of stroke. However, the role of atopic diseases/diathesis in the risk of stroke among patients with bipolar disorder remains unclear. Methods Using Taiwan’s National Health Insurance Research Database, we selected 55,593 patients with bipolar disorder between 2002 and 2008, divided them into patients with atopic diseases/diathesis (n = 21,050) and patients without atopic diseases/diathesis (n = 34,543), and observed them until the end of 2011. Patients who experienced a stroke during the follow-up period were identified. Results Patients with bipolar disorder and atopic diseases/diathesis had an elevated risk of ischemic stroke (hazard ratio [HR]: 1.44, 95% confidence interval [CI]: 1.25–1.59) compared with patients with only bipolar disorder; a dose-dependent relationship was observed between the number of allergic comorbidities and the risk of ischemic stroke (1 atopic disease, HR: 1.30, 95% CI: 1.13–1.49; 2 atopic diseases, HR: 1.59, 95% CI: 1.33–1.91; 3 atopic diseases, HR: 2.09, 95% CI: 1.50–2.91).The role of atopic diseases in the risk of hemorrhagic stroke among patients with bipolar disorder was nonsignificant (HR: 0.84, 95% CI: 0.64–1.09). Conclusions Patients with bipolar disorder and atopic diseases/diathesis are more prone to ischemic stroke later in life than are those without atopic diseases/diathesis. Further study is required to investigate the underlying mechanism linking atopy, bipolar disorder, and stroke.