Collie was born in Insch in Aberdeenshire, Scotland on 2 June 1793 to Alexander and Christina Collie (née Leslie). The youngest of three sons, Collieiu
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 was ship's surgeon on the HMS Sulphur. This was part of the expeditionary group, including the barque Parmelia, which set out from Portsmouth in February 1829 to found the colony of Western Australia. They arrived at Rottnest Island on 3 June 1829. While at sea on 16 April 1829 Collie assisted with the birth of Frederick Henry Stirling son of Lieutenant-Governor (Sir) James Stirling and his wife Ellen.
Upon arriving at Rottnest Island in June 1829, Collie worked in a hospital tent on 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 the conditions on the Peel estate. He 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 was appointed a Justice of the Peace and became the town's first government resident. Suffering from ill health he returned to Perth and was appointed the Swan River Colony's Colonial Surgeon from 1833 to 1835. His decision to return to England was made too late; although he had embarked on the HMS Zebra and he died before the ship left Western Australian waters. He died in King George Sound on 8 November 1835 and was buried beside Mokare his Aboriginal exploring companion.
The graves of both Collie and Mokare were disturbed during the construction of the Albany Town Hall in 1887. Collie's remains were interred at Pioneer Cemetery in Albany.
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 dedication on the monument reads
"To ALEXANDER COLLIE R.N. Physician, Explorer, and Administrator, Who discovered and named the Collie River November 23rd, 1829.
Erected by the Municipal Council of Collie November 23rd, 1935".
Collie Street in Fremantle is also named in his honour.
A Mexican bird species, the black-throated magpie-jay (Calocitta colliei Vigors, 1829), was named after him following his visit to the area on the Blossom in the 1820s.
The Australian turtle species (Chelodina colliei Gray, 1856) is also named in honour of Collie.