He attended McGill University, where he initially intended to study law, but became interested in geology after accompanying a friend on a summer field expedition to Labrador. He subsequently earned bachelor's, master's, and Ph.D. degrees in geology, completing his studies between 1928 and 1933.
After completing his studies, Williamson travelled to South Africa with one of his professors, where he eventually took a job with Loangwa Concessions, a De Beers subsidiary in what was then Northern Rhodesia (now Zambia). He then moved on to work at the Mabuki diamond mine, which he purchased from the owners in 1936 when they had decided to shut the mine down. Williamson struggled to support himself with the operations of the Mabuki mine, while using it as a base for diamond prospecting in the region.
In 1940, he discovered the diamond-bearing kimberlite pipe at Mwadui that he would develop over the coming years into the Williamson diamond mine. The diamond mine at Mwadui was closely managed by Williamson, who by the 1950s had developed a diamond mining operation renowned for its efficiency and technological innovations. By 1952 the mine was operating at 10,000 tons per day.
The mine's production, which Williamson owned in full, made him one of the richest men in the world by the time of his death in 1958 of cancer. The mine, famous for being the first significant diamond mine outside of South Africa, continues to operate today, and the total production from 1941-2008 has been estimated at 20 million carats (4,000 kg) of diamonds. The mine produced many fine gems including the Williamson pink diamond, a pink 23.6 carats (472 g) rough diamond presented to Princess Elizabeth and Prince Philip on their wedding day in 1947.
It became the centrepiece of the Williamson Diamond brooch made for the Queen in 1952. The life of John Williamson was adapted into the biographical novel The Diamond Seeker by John Gawaine (a pen name), which was published in 1967. The book depicts Williamson as quiet to the point of secretive, and something of a womanizer.
However, it also hails him as the last of the great diamond prospectors, who were able to find meaningful deposits and establish significant, successful mines without outside resources or support. While the book is known to have taken some liberties with the facts, it is one of the few biographical sources available. Williamson was inducted into the Canadian Mining Hall of Fame on January 13, 2011.