This comparison of institutions of science advice during COVID-19 between the Westminster systems of England/UK and Ontario/Canada focuses on the role of science in informing public policy in two central components of the response to the pandemic: the adoption of non-pharmaceutical interventions (NPIs) and the procuring of vaccines. It compares and contrasts established and purpose-built bodies with varying degrees of independence from the political executive, and shows how each attempted to manage the tensions between scientific and governmental logics of accountability as they negotiated the boundary between science and policy. It uses the comparison to suggest potential lessons about the relative merits and drawbacks of different institutional arrangements for science advice to governments in an emergency.