With an injury to Channing Frye, Lee started his first game of the season against the Chicago Bulls on November 28, 2006. On December 16, 2006, he was one of 10 players ejected in the Knicks–Nuggets brawl. However, he was not involved in the brawl and was not suspended by the NBA. On December 20, 2006, in a double-overtime game against the Charlotte Bobcats with 0.1 seconds left, Lee scored the winning basket by tipping in an inbounds pass. This was within the league's so-called Trent Tucker Rule, whereby a player cannot catch and shoot a successful field goal with less than three-tenths of a second remaining on the clock. At the All-Star break, Lee had averaged 11.1 points on 61.05% shooting (first in the league), an 80.0% free throw percentage, 10.8 rebounds (8th in NBA) and 1.8 assists in 30.9 minutes a game. On February 16, 2007, Lee, playing for the Sophomores, was named the Most Valuable Player in the Rookie Challenge, finishing with 30 points on 14 of 14 shooting from the field and 11 rebounds. On February 23, 2007, in a game against the Milwaukee Bucks, Lee came down on future teammate Andrew Bogut's foot and sprained his ankle. The original diagnosis was for him to only miss a few days, but nearly three weeks after the injury he was still unable to play. He was reexamined and the doctor found that he had a much more severe sprain than was originally diagnosed. Lee played only sporadic minutes for the remaining games of the season.