Southeastern had 137 student-athletes compete while ineligible over a five-year span.
The university says most of the athletes failed to meet NCAA academic requirements.
"This was a case where student-athletes were erroneously certified as being eligible due to flaws in the eligibility certification process" said Athletics Director Bart Bellairs. "In many instances, student-athletes would have been eligible had proper procedure been followed, such as timely declaration or change of a major.
According to reports, most of the violations happened during the 2005-2006 and 2006-2007 school years.
The school says no staff members involved with the violations are still with the school and that no current student-athletes are involved.
"This was not a case in which student-athletes who lacked academic preparation and ability were recruited to the university," Bellairs added. "86 percent of the student-athletes identified in the case went on to graduate from Southeastern or left the university in good academic standing."
Southeastern has self-imposed penalties, including vacating wins from games in which ineligible players participated, scholarship reductions and two years of probation.