John Thompson joined the Mercyhurst College coaching staff in 2007 as the team's defensive backs coach. He was promoted to defensive coordinator in the spring of 2008.

Coach Thompson spent six years at Sacred Heart, serving as the Defensive Coordinator/Defensive Backs Coach from 2002-2005. His first two years he served as the Special Teams Coordinator/Defensive Line Coach. During the 2000 season, the Pioneers had what ties for the largest turnaround in NCAA history, improving from 2-9 the previous season to 10-1. Sacred Heart won the Mid-Major I-AA Championship the next year, going 11-0 and defeating Duquesne in the ECAC Bowl.

Prior to Sacred Heart, Thompson coached for two years at St. Francis (Pa.), where he coached linebackers and defensive backs.

Thompson started his coaching career at Marist, his alma mater. In 1997, the Red Fox backfield was part of a defensive unit that ranked first in the nation and set two NCAA records for yards per carry and rushing yards per game.

Thompson graduated from Marist in 1994 with a degree in Business/Human Resources. The Rome, New York. native was a four-year member of the Red Fox football team.