WEHI’s National Drug Discovery Centre (NDDC) is a cutting-edge high-throughput screening (HTS) facility that uses robotic platforms to rapidly identify bioactive compounds during the early stages of drug discovery. This state-of-the-art facility provides the ability to screen libraries of hundreds of thousands of drug-like compounds against medically relevant biomolecules and biological systems. The NDDC offers subsidised screening to Australian researchers through a competitive application process, thanks to generous financial support from WEHI, the Australian and Victorian Governments, and philanthropic donors. The recent breadth and severity of the global SARS-CoV-2 pandemic have created an urgent need for the development of therapeutics to prevent infection and to treat the virus. The SARS-CoV-2 Main protease (Mpro) is a virally encoded protease that mediates cleavage of the SARS-CoV-2 polyprotein. Mpro function is essential for productive SARS-CoV-2 infection and it is considered to be one of the most attractive targets for the development of drugs to treat COVID-19. At the NDDC, we have identified novel inhibitors of Mpro by screening a library of over 400,000 small molecules. Here, we present the production of recombinant Mpro, the development of an HTS-amenable FRET-based assay, and the utilisation of this assay in the pilot, primary, and confirmation compound screening. The discovery of potent inhibitory molecules from this screen provides a starting point for the development of new drugs as therapies in the treatment of COVID-19. Our project to identify Mpro inhibitors illustrates the use of the NDDC for HTS and will be of special interest to researchers seeking to access this facility.