Lee starred in both football and baseball at St. Ignatius College Preparatory in San Francisco. He was a three-year all-league quarterback in high school, but focused much of his time on baseball, limiting his Division I football scholarship offers out of high school. Lee chose Nebraska after also receiving strong recruiting interest from Oklahoma, Fresno State and Mississippi State among others.
Lee played 2 seasons at the City College of San Francisco. He came to Nebraska following a highly successful 2006 season at City College of San Francisco. Lee had a standout campaign for Coach George Rush, with more than 3,400 passing yards and 35 touchdowns while completing 64 percent of his passes. Lee's performance led City College of San Francisco to a 10-2 record and an appearance in the California junior college title game. The City College of San Francisco offense averaged nearly 40 points per game with Lee at QB. Lee was ranked as the nation's top junior college quarterback by Rivals.com, Scout.com and SuperPrep Magazine. Lee sat out the 2005 season before enrolling in junior college in January 2006. He redshirted his first year at Nebraska in 2007. In 2008, he completed 1 pass for 5 yards and rushed for 17 yards. In 2009, Lee passed for 2,143 yds completing 59% and rushing for 171. He started all 12, led a comeback against Missouri and hit 76% against all Sun Belt Teams. But when he played CT and Missouri, hit just 40 and eventually he lost his job to QB Cody Green. Green ended up only starting 2 and Lee got his job back while guided his team to a Holiday bowl win and #14 ranking. The next season, he began as the starter but was eventually beat out by redshirt freshman Taylor Martinez.