We develop empirical bootstrap data envelopment analysis models to evaluate the relative efficiencies of Saskatchewan’s various health regions in handling the health emergency situation created by the coronavirus (COVID-19) pandemic. Each region’s relative success in managing the influx of COVID-19 cases was assessed based on input and output variables associated with efficiency. Our findings show that Saskatchewan has done a good job of handling the COVID-19 pandemic from a managerial point of view, but not in terms of the effective utilization of resources. We further use the data envelopment analysis models to identify the most efficient health regions, which in turn serve as benchmarks that the other regions can follow in improving their respective efficiencies. The findings of this study can assist decision makers in developing policies that will enable efficient management of the pandemic, and mitigate health inequities for populations in different health regions.