The resignation of Superintendent Joe Cipp, Jr. was announced during the South Country Central School Board meeting.
A preliminary report alleged the grades for Bellport High School athlete Ryan Sloan were altered to qualify the football star for an NCAA scholarship to Syracuse University.
Sloan's football coach was Cipp at the time and the report says that he was likely either involved or knew what was going on.
The investigation began after Bellport principal Kevin O'Connell said he was fired for failing to raise the student's marks. O'Connell has since filed a wrongful termination suit against the South Country Central School District.
Cipp denies he was part of any wrongdoing.
Sloan, a freshman at Syracuse University and member of the school's football team, has declined to comment on the case, but says he worked hard to improve his grades.
The agreement calls for Cipp to resign effective May 2, 2012. After that date, he will be reassigned to other duties.
The School Board will pay Cipp his salary for the next two years, which they say is less then legal fees would have cost if he didn't resign. They say fees would have cost around $1 million, a "substantial" cost to the district.
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