In 1970, Butler was appointed a Member of the Order of the British Empire. In 1980 this was upgraded to Commander level (CBE). In 1979, Butler was named the Australian of the Year, jointly with Neville Bonner. In 1993, he was awarded a cash prize for his 30 years of work with the petroleum industry. On 4 March 2012, he was added to the National Trust of Australia's National Living Treasures list. On 11 June 2012, he was named an Officer of the Order of Australia for "distinguished service to the community through the promotion of public understanding of natural history and wildlife conservation, to the development of collaborative environmental partnerships with industry, and to the community." A species of mulga snake, Pseudechis butleri, and a spider, Synothele butleri, are named for Butler. Three species of Australian lizards are named for Butler: Delma butleri, Morethia butleri, and Notoscincus butleri. Two species of Australian lizards are named for Butler and his wife, Margaret Butler: Ctenophorus butlerorum and Eremiascincus butlerorum. On 17 April 2016, the new Western Australian Museum research facility and storage centre in Welshpool was named in his honour. The Harry Butler Institute was established in August 2017 at Murdoch University in partnership with Chevron to help shape a new generation of leaders in conservation and environmental management. The Harry Butler Science Centre, named in honour of the Australian environmental pioneer, was officially opened on Barrow Island in June 2018 by Chevron and Murdoch University as partners of the University's Harry Butler Institute.