Lee's Reserve team performances were rewarded in the 2006–07 season by him being given the captain's armband. In between his 25 appearances for the Reserves that season, Lee also made his first team debut. He was named as a substitute in the League Cup Third Round tie against Crewe Alexandra and, with the score at 1–1, he came on for David Gray in the 77th minute. The match went to extra time and, with less than two minutes remaining, Lee made a charging run up from right back to latch onto an Alan Smith through-ball. He composed himself, and slid the ball coolly past Crewe's former Manchester United goalkeeper, Ben Williams.