Background: and Purpose Changes to hospital systems were implemented from March 2020 in Australia in response to the coronavirus disease 2019 pandemic, including decreased resources allocated to stroke units. We investigate changes in the quality of acute care for patients with stroke or transient ischemic attack during the pandemic according to patients’ treatment setting (stroke unit or alternate ward). Methods: We conducted a retrospective cohort study of patients admitted with stroke or transient ischemic attack between January 2019 and June 2020 in the Australian Stroke Clinical Registry (AuSCR). The AuSCR monitors patients’ treatment setting, provision of allied health and nursing interventions, prescription of secondary prevention medications, and discharge destination. Weekly trends in the quality of care before and during the pandemic period were assessed using interrupted time series analyses. Results: In total, 18,662 patients in 2019 and 8,850 patients in 2020 were included. Overall, 75% were treated in stroke units. Before the pandemic, treatment in a stroke unit was superior to alternate wards for the provision of all evidence-based therapies assessed. During the pandemic period, the proportion of patients receiving a swallow screen or assessment, being discharged to rehabilitation, and being prescribed secondary prevention medications decreased by 0.58% to 1.08% per week in patients treated in other ward settings relative to patients treated in stroke units. This change represented a 9% to 17% increase in the care gap between these treatment settings during the period of the pandemic that was evaluated (16 weeks). Conclusions During the first 6 months of the pandemic, widening care disparities between stroke units and alternate wards have occurred.