Dr. Dain Butler's resignation followed a closed-door meeting Monday morning.
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Chief Student Services Officer Kristy Davis has been named as acting superintendent.
Butler will receive a severance payment of $102,000. His resignation was effective at the end of the business day Monday. The school board also agreed to pay Butler an additional amount of up to $116,362 if certain conditions are met.
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The move is the latest shakeup at central office as the district deals with financial and legal troubles.
In February, ABSS parted ways with Chief Financial Officer Kim McVey. Deputy Superintendent Lowell Rogers, who took over as interim CFO, was then suspended a day later after he was charged with failure to report alleged child abuse to law enforcement.
The district has also been dealing with mold issues that delayed the start of the current school year. The district has spent millions on mold removal and cleanup efforts.