Men's sports include baseball, basketball, cross country, golf, lacrosse, soccer, tennis, and track and field; while women's sports include basketball, cross country, golf, lacrosse, soccer, softball, tennis, track and field, and volleyball.

Baseball coach Rick Robinson earned his 500th win at Young Harris in April 2009, and had been highly successful in placing players in Division I schools.

However, the program remained dormant until November 13, 2010, when the sport returned after a 40-year absence, led by former Georgia interim head coach Pete Herrmann.

In 1998, led by former coach Jim Thomas, the Mountain Lions won the 1998 NJCAA Division I State Soccer Title.

Women's basketball began at Young Harris on November 15, 2010, led by former Mississippi State head coach Brenda Paul.

Conference tournament champion The Young Harris Lady Mountain Lions won the 2006 NJCAA Division I Women's Soccer National Championship, under head coach Kathy Brown.

Brown originally served as the assistant coach at Jacksonville State before coming to Young Harris in 1997 and starting the women's soccer program.

[18][19] The program is currently led by former Young Harris men's soccer athlete and assistant under Kathy Brown, Avram Allen.