Collie was born in Insch in Aberdeenshire, Scotland on 2 June 1793 to Alexander and Christina Collie (née Leslie). The youngest of three sons, Collie studied medicine in Edinburgh before moving to London to further his studies. In January 1813, he joined the Fellowship of the Royal College of Surgeons and became an assistant surgeon in the navy.
He sailed on the frigate Doris to Tenerife, China and the East Indies, before returning to Europe to study botany, mineralogy and chemistry. In 1824 he was a surgeon on board the HMS Blossom and travelled to Africa, Brazil, Chile, the Sandwich Islands, California, Kamchatka Peninsula, Taiwan and Mexico.
Collie joined the HMS Sulphur's February 1829 expedition to Western Australia, where he assisted with the birth of James Stirling and his wife Ellen's child, Frederick Henry, while at-sea. Upon arriving at Rottnest Island in June 1829, Collie worked in medical tent at Garden Island and studied botany in his free time. He received 1,500 acres (610 ha) of land on the banks of the Swan River.
He and Lieutenant Preston explored the south west of Western Australia, discovering two rivers that Lieutenant Governor Stirling named after them: Collie River and Preston River. In 1830 he investigated Peel estate and reported that the estate's manager, Thomas Peel, was incompetent, which led to government assistance for the settlers.
In 1831, Collie was allotted 500 acres (200 ha) of land in Albany, where he became the town's first government resident. He returned to Perth to be the Swan River Colony's Colonial Surgeon from 1833 to 1835. He died at King George Sound on 8 November 1835.
The town of Collie and Collie River are named in his honour in Western Australia, with a granite monolith erected for him in Collie. The Mexican Jay Calocitta colliei was named after him following his visit to the area on the Blossom in the 1820s.
- Chessell, Gwen (2008). Alexander Collie: Colonial Surgeon, Naturalist and Explorer. Perth: University of Western Australia Press. ISBN 0-9802965-3-6.