The first edition of the genomics costing tool (GCT) facilitates budgeting and resource mobilization for infrastructure, workforce, biosafety and quality assurance associated with SARS-CoV-2 genomic surveillance. This tool will be useful to country, regional and global policymakers, health administrators and economists, laboratory directors, quality managers, donor institutions and other stakeholders engaged in genomic surveillance for priority pathogens. The GCT is a Microsoft Excel-based tool which is accompanied by a user manual to guide its users.