Raised in rural Ontario, Thomson was born into a large family of farmers and displayed no immediate artistic talent. He worked several jobs before attending a business college, eventually developing skills in penmanship and copperplate writing. At the turn of the 20th century, he was employed in Seattle and Toronto as a pen artist at several different photoengraving firms, including Grip Ltd. There he met those who eventually formed the Group of Seven, including J. E. H. MacDonald, Lawren Harris, Frederick Varley, Franklin Carmichael and Arthur Lismer. In May 1912, he visited Algonquin Park—a major public park and forest reservation in Central Ontario—for the first time. It was there that he acquired his first sketching equipment and, following MacDonald's advice, began to capture nature scenes. He became enraptured with the area and repeatedly returned, typically spending his winters in Toronto and the rest of the year in the Park. His earliest paintings were not outstanding technically, but showed a good grasp of composition and colour handling. His later paintings vary in composition and contain vivid colours and thickly applied paint. His later work has had a great influence on Canadian art—paintings such as The Jack Pine and The West Windhave taken a prominent place in the culture of Canada and are some of the country's most iconic works.
Thomson developed a reputation during his lifetime as a veritable outdoorsman, talented in both fishing and canoeing, although his skills in the latter have been contested. The circumstances of his drowning on Canoe Lakein Algonquin Park, linked with his image as a master canoeist, led to unsubstantiated but persistent rumours that he had been murdered or committed suicide.