Clark was appointed an Officer of the Order of Australia on Australia Day 2013 "for distinguished service to science and technology through leadership and governance of the scientific community of the Australian Defence Force and through contributions to quantum computing and nanotechnology". and was awarded the Centenary Medal on 1 January 2001 "for contribution to world leading research in the field of quantum computing and physics". He is a Fellow of the Australian Academy of Science (2001), a Distinguished Fellow of the Royal Society of New South Wales (2009), and has received numerous other acknowledgements and awards.