After his playing career ended, Lynch initially accepted a position as a graduate assistant on the Ball State coaching staff, but instead decided to accept a position at
Saint Joseph's College in
Rensselaer, Indiana as the offensive coordinator and quarterbacks coach. He held this position for one year before joining the coaching staff at
Ashland University as the offensive coordinator in 2008.
Ball State Lynch joined the coaching staff at his alma mater
Ball State as a wide receivers coach in 2009, and was later named the recruiting coordinator in 2010. He was retained by newly hired head coach
Pete Lembo in 2010 and shifted to coaching the tight ends position and recruiting coordinator for the 2011 season. He was promoted to offensive coordinator and quarterbacks coach in December 2013 after
Rich Skrosky accepted the head coaching position at
Elon. Lynch added the title of assistant head coach in 2019. He was named a
Broyles Award nominee in 2019 after guiding Ball State to a top 25 offense in terms of total yards.
Colorado State Lynch was named the offensive coordinator at
Colorado State in 2020.
Vanderbilt Lynch was hired as the quarterbacks coach and passing game coordinator at
Vanderbilt under first-year head coach
Clark Lea. Following the 2023 season, it was announced that Lynch would not return to the program for 2024.
Texas A&M Lynch later joined
Texas A&M as a senior offensive analyst in January 2024. He was promoted to quarterbacks coach on January 1st, 2026, after the departure of offensive coordinator
Collin Klein. == Personal life ==