Snyder resigned as coach on February 10, 2006 following a 26-point loss to Baylor that extended a losing streak to six and dropped the Tigers to a 10-11 record overall, 3-7 in the Big 12. He finished with a 126-91 record over seven years, reaching the NCAA tournament in each of his first four seasons but posting only a 42-42 record since. After his resignation, Snyder accused Missouri athletic director Mike Alden of sending Gary Link, a basketball analyst and assistant to Alden, to inform him that he would be fired after the season.
Following his departure from Missouri in 2006, Snyder initially gave up on coaching for good. But in May 2007, he accepted the head coaching position of the Austin Toros in the NBADL