He then served as the head coach of the Bates Bobcats (2009–2010) and Eastern Kentucky Colonels (2016–2020).
On July 23, 2008, Thompson was named the head coach of the Bates Bobcats baseball team.
[1] After leading the Bobcats to 11–22 and 25–11 during the 2009 and 2010 seasons respectively, Thompson signed to take an assistant coaching position with the Duke Blue Devils baseball team.
[2] After two seasons at Duke, Thompson became the top assistant for the Georgia State Panthers baseball program.
In July 2015, Thompson was named the head coach of the Eastern Kentucky Colonels baseball team.