McGee was selected by the Dallas Cowboys in the fourth round (101st overall) of the 2009 NFL Draft. He became the first quarterback drafted by the Cowboys since Quincy Carter in 2001, and the second since 1991. The Cowboys believed him to be a project, since he was mostly employed as an option quarterback, but had the athletic traits and work ethic to succeed. He signed a four-year deal on July 28. He suffered a sprained right medial cruciate ligament, while throwing his first touchdown in the third preseason game against the San Francisco 49ers, forcing him to miss the possibility of considerable playing time in the final preseason contest against the Minnesota Vikings. In the regular season, he was the third-string quarterback and was declared inactive in all 16 games and two playoff contests.