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

The Flames were also members of the National Christian College Athletic Association (NCCAA), primarily competing as an independent in the Mid-East Region of the Division I level.

Club sports are offered such as boxing, men's and women's rugby, spikeball and ultimate frisbee.

Lee's women's cross country team won three GSC Championships in a row (2017, 2018, and 2019), as well as a South Region title in 2019.

Lee's Lady Flames and men's soccer team both won the NCCAA National Championship in 2014.