The San Ysidro school district accepted the resignation of Superintendent Manuel Paul Thursday night.
The board voted 3 to 2 with trustees Yolanda Hernandez and Antonio Martinez casting dissenting votes to accept the resignation.
Paul's letter of resignation was dated March 18, but the district agreed to pay him through the end of the school year, June 30.
Paul was placed on paid leave Jan. 15 after he was indicted by a San Diego County Grand Jury on corruption charges.
The superintendent is the subject of a separate federal investigation into a cash exchange he made with a contractor in the parking lot of a Chula Vista steak house.
He admitted under oath - as part of a separate and unrelated lawsuit - that he took $2,500 in cash from a contractor who was trying to get work with the district.
