Thornton was drafted in the first round (3rd overall) by the Toronto Maple Leafs in the 1989 NHL Entry Draft. He played thirty-three games for the team his rookie season, accumulating one goal and three assists. He also played left wing for the Edmonton Oilers, Montreal Canadiens, Dallas Stars and San Jose Sharks.
He was signed by San Jose as a free agent on July 1, 2000. In his first season with San Jose, he had a career year, scoring twenty goals playing alongside gritty centre Mike Ricci.