Whaley was selected by the Utah Jazz with 51st overall pick in the 2005 NBA draft, becoming the most recent player drafted out of an NAIA school, as of 2018. As a rookie in 2005–06, Whaley appeared in 23 games and averaged 2.1 points and 1.9 rebounds per game. He scored a career-high 11 points on December 23, 2005 against the New York Knicks. On January 26, 2006, he was ruled out indefinitely with torn cartilage in his right knee. He returned to action in March 2006, but appeared in just one further game after returning to injury.