He entered the Royal Naval College at the age of fifteen, and for nine years served under Phillip Parker King on HMS Adventure and John Franklin in the Mediterranean. In 1836 he sailed to the Arctic as scientific officer on HMS Terror under George Back. In 1838 he was given command of HMS Britomart and sailed to Australia and New Zealand, returning in 1843. In March 1842 he was elected a Fellow of the Royal Society 
In December 1846 Stanley sailed from Portsmouth in charge of HMS Rattlesnake, with the naturalists Thomas Huxley and John MacGillivray on board, accompanied by Charles Bampfield Yule in the HMS Bramble In November 1847 he arrived at Port Curtis on the Australian coast, and after surveying the harbour described it as a very good anchorage. In 1848 he continued further north to survey New Guinea, and in June of that year offered protection and assistance to Edmund Kennedy's expedition to the Cape York Peninsula. Owen went on to survey the Louisiade Archipelago but in 1849 fell ill, and died in March 1850 after returning to Sydney.
Thomas Huxley published Diary of the Voyage of the HMS Rattlesnake in 1850 describing the events of the voyage.
The Owen Stanley Range in New Guinea is named after him.
- O'Byrne, William Richard (1849). " Stanley, Owen". A Naval Biographical Dictionary. John Murray. Wikisource.
- European and American voyages of scientific exploration
- "Library and Archive Catalogue". Royal Society. Retrieved 29 December 2010.
- Francis West (1967). "Biography - Owen Stanley". Australian Dictionary of Biography. Retrieved 2014-12-01.
- Quanchi, Historical Dictionary of the Discovery and Exploration of the Pacific Islands, page 234
- Huxley, Julian (ed). T.H. Huxley's diary of the voyage of HMS Rattlesnake. London 1935
- Quanchi, Max (2005). Historical Dictionary of the Discovery and Exploration of the Pacific Islands. The Scarecrow Press. ISBN 0810853957.
- MacGillivray, John Voyage Of HMS Rattlesnake
- Volume I: Gutenberg Project EText num 12433, ISBN 978-1-4065-2973-9
- Volume II: Gutenberg Project EText num 12525, ISBN 978-1-4021-7207-6,
- Stanley, Owen (1811-1850) National Library of Australia, Trove, People and Organisation record for Owen Stanley
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