|Alma mater||Cleveland State '98|
|Coaching career (HC unless noted)|
|2000||Saint Rose (asst.)|
|2001–2002||George Washington (asst.)|
|2003–2004||Kent State (asst.)|
|2005–2006||NC State (asst.)|
After completing his playing career, Waggoner began coaching at Saint Rose in Albany, New York. In his one season with the Golden Knights, they reached the Division II College World Series. He then landed an assistant coaching position with George Washington. The Colonials set a school record for wins (42), won the Atlantic 10 Conference championship, and were among the national leaders in many offensive categories in 2002. Waggoner then moved to Kent State for two seasons. The Golden Flashes claimed the 2004 Mid-American Conference Baseball Tournament and saw seven players picked in the Major League Baseball Draft. He moved to NC State next, where he served as recruiting coordinator, as well as managing player development, academic support and travel, preparing him well for his future head coaching duties. The Wolfpack appeared in the NCAA Tournament during both seasons, finished second in the 2006 Atlantic Coast Conference Baseball Tournament, and produced two All-Americans.
In the summer of 2006, Waggoner was named head coach at Marshall of Conference USA. During his time at Marshall, 24 players have signed professional contracts, and the Thundering Herd set a program record for wins with 30 in 2008. The 2008 season also saw him named Coach of the Year by Collegiate Baseball Newspaper.
Head coaching records
|Marshall (Conference USA) (2007–present)|
National champion Postseason invitational champion
- "Jeff Waggoner Profile". herdzone.com. Retrieved December 21, 2012.
- "Marshall University Hires Jeff Waggoner as Head Baseball Coach". herdzone.com. August 18, 2006. Retrieved December 22, 2012.
- "Herd's Jeff Waggoner Named Coach Of The Year". scout.com. June 23, 2008. Retrieved December 22, 2012.
- "2013 Conference USA Baseball Media Guide" (PDF). Archived from the original (PDF) on 9 February 2013. Retrieved 9 February 2013.
- "2013 Conference USA Baseball Standings". D1Baseball.com. Jeremy Mills. Archived from the original on May 21, 2013. Retrieved May 20, 2013.