Thompson attended University High School in Tucson, Arizona from 1999 to 2003. While there he won the Class 4A state team championship in 2003, and was named the Arizona High School State Player of the Year in 2002 and 2003. Thompson attended Tulane University two seasons until they disbanded their golf team after Hurricane Katrina. Thompson then transferred to the University of Alabama. While playing on Alabama's golf team, Thompson was the 2008 SEC Player of the Year.