In 2007 Stephen was elected a Fellow of the Australian Academy of Science, in 2008 he was awarded the Eureka Prize for Scientific Research, in 2009 he was named NSW Scientist of the Year, and in 2010 he was named as the Wigglesworth Medallist by the Royal Entomological Society of London, of which he was made an Honorary Fellow. He was also co-writer, narrator and presenter of the four-part documentary Great Southern Land, for ABC TV, which was aired to critical and viewer acclaim in September 2012.

In 2013 Stephen was elected a Fellow of the Royal Society of London as “one of the world’s foremost entomologists and nutritional biologists”, and in 2015 he was made a Companion of the Order of Australia “for eminent service to biological and biomedical science.”