Brian Lee grew up in Moorhead, Minnesota and was a stand out player for the Moorhead High School Spuds hockey team. In 2004–05 Lee played junior hockey for the Lincoln Stars of the USHL and had an outstanding season. For his season, he was selected Minnesota's Mr. Hockey as the number one player in Minnesota high school boys hockey in 2005. He was also named the Associated Press' Player of the Year for Minnesota prep boys hockey that year. That year, his senior year, he was one of the few high school players to play for Team USA in the World Junior Hockey Championships.