In June 2021, Courtney was asked his views on the vaccination of children to protect against Covid-19. He told the Daily Telegraph, "If JCVI look at the ethical questions and if they think on the ethical balance – and the MHRA say there is a high degree of safety – then in an ideal world we think it would be better if kids were vaccinated and had three weeks immunity before they come back to school in September." He recognised there were "ethical questions" because children "don't by and large get seriously ill", adding: "So if there is a risk from the vaccine, even if it is an incredibly small risk, an ethical question is raised about whether you give them something with a risk." When the JCVI declined to back mass vaccinations for 12-15 year olds in September 2021, he said “this makes additional safety mitigations in schools all the more important.”