Embattled St. Francis Schools Superintendent Edward Saxton, accused of inflating enrollment numbers to collect additional state dollars for his district, resigned Monday after a settlement in which he’ll receive $150,000 in back sick leave, vacation and holiday pay.

Saxton had been on paid leave since January 2014, collecting $186,000 in salary over those 15 months, as the district tried to fire him, resulting in a court battle.

The settlement, approved Monday night by the St. Francis school board, includes dismissal of all pending litigation. Saxton’s resignation also means the northern Anoka County district will not pay out the final year of his three-year contract.

“It was a year that could have gone very badly. I am glad to be done with it,” said school board Chairman David Roberts.

Roberts said Saxton’s payout includes sick and holiday pay accrued during his 20-year employment with the district, where he became superintendent in 2003 after serving as high school principal, among other jobs.

“It’s about 10 years’ worth,” Roberts said.

St. Francis Schools has also agreed to repay the state $475,000 in per-pupil funding after a Minnesota Department of Education audit concluded the district miscalculated student enrollment by as many as 53 students for three years during Saxton’s tenure.

Saxton’s attorney, Roger Aronson, did not return a call for comment Tuesday but has denied that his client misled local or state leaders.

At issue was a program Saxton created called 21st Century Learning. The sprawling rural district provided home-schooled students laptops and access to technology and teachers, then claimed the students for full-time reimbursement from the state.

The district receives about $38 million in state aid each year for its more than 5,000 students. Its annual operating budget is around $50 million.

Interim Superintendent Troy Ferguson said the district is repaying the full amount this school year.

“We are not writing them a check. We are taking that much less in aid this year to pay for it. That will be done June 30 of this year,” Ferguson said. “We knew it might be coming and we planned for it in our budget this fiscal year.”

Saxton’s actions are still the subject of a pending inquiry by the Anoka County Sheriff’s Office, which is investigating whether they constituted a crime. There are no allegations that Saxton gained personally.

Documents filed in Anoka County District Court alleged that Saxton misled the St. Francis school board and Minnesota Education Commissioner Brenda Cassellius about 21st Century Learning. The school board placed Saxton on paid leave Jan. 21, 2014, and ordered an outside investigation. The board tried to fire him in March 2014 for an “ongoing pattern of misconduct.”

Saxton appealed and an arbitrator ruled last fall that he should be reinstated. The school board kept Saxton on leave and challenged the arbitrator’s ruling.

The district had previously alleged: “The 21st Century Program provided minimal support and services to students and their families, despite the fact that the District collected full-time reimbursement for students in the program,”

When the Department of Education raised questions, Saxton “provided misleading information” to its staff and Cassellius, the district alleged.

The board also said it was misled by Saxton.

Ferguson said the district disbanded 21st Century Learning and is setting up a new online learning program, pending the state Department of Education’s approval.

“We are very excited about the possibility,” Ferguson said. “Some kids really like the online options. For whatever reason the traditional schedule doesn’t work for some kids.”