Michael Thompson played golf for University High School in Tucson, Arizona from 1999 to 2003 where he won the Class 4A state team championship in 2003 and was named the Arizona High School State Player of the Year in 2002 & 2003. Thompson then transferred to the University of Alabama where he was the 2008 SEC Player of the Year. He represented the U.S. at the 2008 Palmer Cup, and due to his finish as a 2007 U.S. Amateur finalist, earned an invitation to the 2008 Masters Tournament and the 2008 U.S. Open.
Thompson spent one week as number one in the World Amateur Golf Ranking before turning professional in July 2008. In 2010, Thompson was named Hooters Tour Player of the Year and in 2011, he earned his PGA Tour card. In 2012, he finished T2 at the U.S. Open and started off 2013 strong by claiming victory at the Honda Classic.