Prior to his junior season, Lee transferred to Brenham High School as his father, Stephen, took a job on the staff as the wide receiver coach.

Lee holds every major season and career passing record in Brenham High School football history.

Recruiting analyst Tom Lemming compared Lee to former Sam Houston State quarterback Rhett Bomar.

[2] Lee had more than 30 scholarship offers from Division I schools, and chose to attend LSU over Nebraska, Kansas State, Oklahoma, and others on May 30, 2006.

[3] Sources: Lee was the third-string quarterback at LSU behind then-senior Matt Flynn and redshirted sophomore Ryan Perrilloux.

[8] In his only start of the 2009 season, Lee completed 7-of-22 (32%) passes in a homecoming game win against Louisiana Tech, a member of the Western Athletic Conference.

[11] Although Lee did not start any games, he was called on to lead game-winning drives against Tennessee, Florida, and Auburn.

He drove LSU down to the 2 yard line against Tennessee, threw a game-winning touchdown pass against Florida, but failed against Auburn.

[13] In the season opener against #3 Oregon, Lee helped lead LSU to a 40–27 victory although completing only 10 of 22 (45%) passes for less than 100 yards.

The decision to give the starting role back to Jordan Jefferson was not without some controversy,[23] and was questioned by some media and fans throughout the rest of the season.

This caused heated exchanges from some fans and media, with the sharpest public criticism coming from Bobby Hebert in a post-game outburst where he demanded to know why Miles did not put Lee into the game.