NCAA Division II independent schools are four-year institutions that are not formally affiliated with any athletic conference. Schools that are members of a conference may also field intercollegiate teams in football, lacrosse, soccer, wrestling, and other sports not affiliated with a conference, usually due to their primary conference not having enough teams in a certain sport to enable sponsorship of the sport by that conference.
|Bluefield State College||Bluefield, West Virginia||1895||1,800||Big Blues & Lady Blues|
|Emory & Henry College||Emory, Virginia||1836||1,250||Wasps|
|University of Puerto Rico at Bayamón||Bayamón, Puerto Rico||1971||5,014||Cowboys|
|University of Puerto Rico at Mayagüez||Mayagüez, Puerto Rico||1911||12,079||Bulldogs|
|University of Puerto Rico, Río Piedras||San Juan, Puerto Rico||1903||15,186||Gallitos & Jerezanas|
|Salem University||Salem, West Virginia||1888||835||Tigers|
Men's sponsored sports by school
|Emory & Henry||7|
|UPR Río Piedras||5|
Women's sponsored sports by school
|Emory & Henry||8|
|UPR Río Piedras||5|
Other sponsored sports by school
- ‡ — D-I sport
|Barton College||Wilson, North Carolina||Bulldogs||Carolinas|
|Bluefield State College||Bluefield, West Virginia||Big Blues||None|
|Emory & Henry College||Emory, Virginia||Wasps||South Atlantic (in 2022)|
|Erskine College||Due West, South Carolina||Flying Fleet||Carolinas|
|Post University||Waterbury, Connecticut||Eagles||Central Atlantic|
- Barton — South Atlantic Conference scheduling alliance for the 2020–2021 seasons. Joining the conference as football associate in 2022.
- Erskine ��� Joining the South Atlantic Conference also as football associate in 2022.
|Allen University||Columbia, South Carolina||Yellow Jackets||Southern Intercollegiate|
|Bluefield State College||Bluefield, West Virginia||Lady Blues||None|
|Emory and Henry College||Emory, Virginia||Wasps||South Atlantic (in 2022)|
|Shaw University||Raleigh, North Carolina||Bears||Central Intercollegiate|
|Alderson Broaddus University||Philippi, West Virginia||Battlers||Mountain East|
|Molloy College||Rockville Centre, New York||Lions||East Coast|
|St. Thomas Aquinas College||Sparkill, New York||Spartans||East Coast|
Swimming & diving
|Bluefield State College||Bluefield, West Virginia||Big Blues & Lady Blues||None|
|Roberts Wesleyan College||North Chili, New York||Redhawks||East Coast|
|University of Puerto Rico at Mayagüez||Mayagüez, Puerto Rico||Bulldogs||None|
|Simon Fraser University||Burnaby, British Columbia||TBC||Great Northwest|
Sports not in D-II
- Reclassifying institution in yellow.
|Emory and Henry College||Emory, Virginia||Wasps||South Atlantic (in 2022)||Women's volleyball||2021|
- "Barton, South Atlantic Conference agree to football scheduling alliance". The Wilson Times. January 18, 2019. Retrieved March 20, 2019.