Born in Toronto, he graduated from Malvern Collegiate Institute and attended the Ontario Agricultural College (now the University of Guelph) for one year. He served with the Canadian military in Europe during World War I; after the war ended, he visited many of the top courses in the British Isles. When he returned to Canada after the war he became a full-time golf course architect, going into business himself by 1923. In the 1920s there was a rapid expansion of golf and new courses were needed to accommodate the millions of new players, so Thompson and his peers were kept very busy.
He designed courses from 1912-1952, mostly in Canada, with a philosophy of preserving the natural lay and flow of the land. He got his start with George Cumming, longtime professional at the Toronto Golf Club, who had designed several Canadian courses around the turn of the 20th century.
Thompson's many world-famous courses include the Banff Springs Hotel Golf Course in Banff, Alberta, the Jasper Park Golf Course in Jasper, Alberta, the scenic Fundy National Park Course in New Brunswick and the Highlands Links in Ingonish, Nova Scotia, all four are publicly accessible and located in Canadian National Parks. Banff Springs and Jasper Park earned him a worldwide reputation. Five outstanding private clubs designed by Thompson are the Capilano Golf and Country Club in West Vancouver, British Columbia, the Edmonton Country Club and the Royal Mayfair Golf Club in Edmonton, Alberta. Niakwa Country Club in Winnipeg, Manitoba, and the St. George's Golf and Country Club in Toronto. In 1948, Thompson was a co-founder, with Donald Ross, of the American Society of Golf Course Architects, and helped to train many top golf course architects, including Robert Trent Jones; Thompson and Jones were partners for several years in the 1930s.
Thompson was an excellent player himself, competing with success many times in the Canadian Amateur Championship, and he had four brothers—Nicol, Frank, Mathew, and Bill—all of whom became outstanding Canadian players in the 1920s. Nicol was the professional at Hamilton Golf and Country Club, while the other four remained top-class amateurs. Frank won two Canadian Amateur titles, while Bill won one.
The Stanley Thompson Society provides a list of 178 courses which Thompson laid out, had constructed, or remodeled through one of the companies that he worked for or managed in the years 1912-1953. Geographically, the courses are located in:
- Canada (144 courses)
- USA (26 courses)
- Brazil (4 courses)
- Colombia (2 courses)
- Jamaica (2 courses)