ObjectiveEstrogen‐containing contraceptives and hormone replacement therapy are used commonly, however, the risks of venous and arterial thrombosis imparted by such medications during COVID‐19 infection or other similar viral infections remain undescribed.MethodsTo assess the risk of venous and arterial thrombosis in patients receiving oral estrogen‐containing therapy (ECT) with COVID‐19 as compared to those receiving non‐estrogen‐based hormonal therapy, we conducted a multicenter cohort study of 991 patients with confirmed COVID‐19 infection, 466 receiving estrogen‐containing hormonal therapy, and 525 receiving progestin‐only or topical therapy.ResultsThe use of estrogen‐containing therapy was found to significantly increase the risk of venous thromboembolism (VTE) following COVID‐19 diagnosis after controlling for age (HR 5.46 [95% CI 1.12–26.7, p = .036]). This risk was highest in patients over age 50, with 8.6% of patients receiving estrogen‐containing therapy diagnosed with VTE compared to 0.9% of those receiving non‐estrogen‐based therapies (p = .026). The risk of arterial thrombosis was not significantly associated with oral estrogen use.ConclusionsThese results suggest that estrogen‐containing therapy is associated with a significantly increased risk of VTE in COVID‐19 patients, especially in older individuals. These findings may guide provider counseling and management of patients with COVID‐19 on estrogen‐containing therapy.