Stein received a number of honours during his career. In 1909, he was awarded the Founder's Medal by the Royal Geographical Society 'for his extensive explorations in Central Asia, and in particular his archaeological work'. In 1909, he was awarded the first Campbell Memorial Gold Medal by the Royal Asiatic Society of Bombay. He was awarded a number of other gold medals: the Gold Medal of the Société de Géographie in 1923; the "Grande Médaille d’or" of the Royal Asiatic Society of Great Britain and Ireland in 1932; and the Gold Medal of the Society of Antiquaries of London in 1935. In 1934, he was awarded the Huxley Memorial Medal of Royal Anthropological Institute of Great Britain and Ireland.