Randy Thweatt was placed on paid administrative leave on April 17 after he was arrested by officials from the State Auditor's Office. The school board changed that to unpaid leave on April 24 after he was indicted on two counts of embezzlement.
He's alleged to have taken a district pickup truck and air-conditioning unit.
Thweatt since filed for retirement, which the Lee County School Board accepted at its meeting on Tuesday, ending his employment with the district. The retirement is retroactive to May 31.
Lee County School Board Attorney Gary Carnathan said criminal charges do not affect eligibility in the state retirement system.
"You can retire if you have the required number of days and years in the retirement system," Carnathan said. "Criminal charges don't have an impact on it."
Thweatt has not yet stood trial on the charges. Efforts to contact him were unsuccessful.
The school district has hired Bobbie Sparks as its interim business manager. Superintendent Jimmy Weeks said Tuesday that the district will remain with the interim manager for some time before seeking to fill the full-time position.
The school district's transportation manager, Ralph Capps, also has been on unpaid administrative leave by the district in connection with the state auditor's investigation. No charges have been brought against Capps.
Judy Hill is serving as interim transportation manager.
The auditor's investigation remains open and ongoing, a spokesperson from the office said Tuesday evening.