John Rae was born on September 30, 1813, in Orphir, Orkney Islands, Scotland, where his father, John Rae (1772-1834), M.D., LL.D, was the local agent for the Hudson’s Bay Company.

He was a surgeon, fur trader, explorer, and author. He received his education at home from a private tutor. As a boy, he learned to sail, shoot, and he spent lots of time outdoors on expeditions to the hills, moors, and sea cliffs. He studied medicine in Edinburgh and qualified as a licentiate of the Royal College of Surgeons of Edinburgh in 1833. He was appointed surgeon to the HBC ship Prince of Wales for the voyage from England to Moose Factory, Ont., where he spent the next ten years as both a clerk and surgeon. He learned from the Cree their methods of travelling and hunting and became an expert in snowshoeing. In 1846-1847, he explored the Gulf of Boothia northwest of Hudson Bay. In 1848-1851, he explored the Arctic coast near Victoria Island. In 1854, he went from Boothia to the Arctic coast and learned the fate of the Franklin expedition. He moved to Hamilton and became a founding member of the Hamilton Scientific Association, which became the Hamilton Association for the Advancement of Literature, Science and Art. In 1860, Rae worked on the telegraph line to America, visiting Iceland and Greenland. In 1864, he made a further telegraph survey in the west of Canada. In 1884, he again worked for the Hudson's Bay Company as an explorer of the Red River for a proposed telegraph line from the United States to Russia. In 2013, The John Rae Society was formed in Orkney to promote Rae's achievements.

In 1860, he married Catherine Jane Alicia Thompson (1838–1919). He died on July 22, 1893, in London, England, and is buried in Kirkwall, Orkney Islands, Scotland.