Kelly began his coaching career as a volunteer assistant for the Cal Poly Mustangs, a job he supplemented while also working at a local grocery store.[4] The following year, he got his first full-time assist job, being named the pitching coach at Chico State.[5] Kelly would reunite with Larry Lee, joining his staff at Cal Poly as the pitching coach.
On August 16, 2012, Kelly was named the pitching coach of the Washington Huskies.[6] Kelly helped elevate Husky pitching, culminating in a 2018 College World Series appearance. For his efforts during that season, he was named d1baseball.com's Assistant Coach of the Year.[7] At the conclusion of the 2019 season, Kelly left the Huskies to take the same position with the Arizona State Sun Devils.[8] Following head coach Tracy Smith's dismissal, Kelly left Arizona State to become the pitching coach of the LSU Tigers.[9]
On June 24, 2022, Kelly was named the head coach of the Washington Huskies.[10]
On June 30th, 2024, it was announced that Kelly would leave Washington to join new Texas A&M baseball coach Michael Earley as the pitching coach.
National champion
Postseason invitational champion
Conference regular season champion
Conference regular season and conference tournament champion
Division regular season champion
Division regular season and conference tournament champion
Conference tournament champion