MALDEN — For more than three years, state education officials have had acrimonious dealings with the leaders of Mystic Valley Regional Charter School over their management style and attempts to expand.

Earlier this year, the state relented and approved the school’s expansion plans. But now the chairman of the school’s Board of Trustees has resigned, citing some of the same problems flagged by state officials as he headed to the exit.

“I don’t think the board was acting in the best interests of the school or the students, and that’s why I didn’t feel like being part of that,’’ Fran Brown said in an interview.

Brown, who served on the board for 14 years, resigned after a June 20 board meeting, when Neil Kinnon was voted back in as chairman. Kinnon had served as chairman for much of the last two decades.

In an interview, Brown said he had worked to mend relations with the state over the past year. During that time, the state lifted its set of conditions and approved the school’s expansion.

With Kinnon returning as chairman, Brown wrote in a LinkedIn post that he feared that the board would overstep its bounds and meddle in the school’s day-to-day management.

“This success and new way of thinking — the board as caretakers of a mission and the administration as the day-to-day workers — did not sit well with those that relished the control,’’ he wrote on LinkedIn. “So after what must have been some careful backroom negotiations, the prior chair was able to secure the votes to win the chair back.’’

Brown’s resignation breaks a period of calm at the school, which has spent the last year working to gain approval to expand. In 2013, when the school applied to expand from 1,500 to 1,900 students, state Education Commissioner Mitchell D. Chester denied the request, citing the board’s “clear record of insularity and opaque decision-making.’’

In his review of the school, Chester noted that all of the trustees had served a minimum of 12 years on the board and were involved in its day-to-day management, which ran against state guidelines.

“The board maintains close involvement in all aspects of the school and is functioning in a management, rather than governance, capacity,’’ the Department of Elementary and Secondary Education concluded in a review of the school in February 2013.

That year, Chester imposed several conditions on the school’s board of trustees. Chester requested that the board amend its bylaws to set term limits, expand to at least seven members, engage in a comprehensive self-evaluation, participate in an educational program on the roles and responsibilities of a school board, and also submit meeting agendas and minutes to the Department of Elementary and Secondary Education.

Kinnon, the returning board chairman, did not respond to interview requests from the Globe.

Mystic Valley, a K-12 school with 1,489 students, opened in 1998 and has a waiting list of 3,600 children. The school has four campuses in Malden, and draws students from Everett, Malden, Medford, Melrose, Stoneham, and Wakefield.

Martin Gately, a school spokesman, did not respond to interview requests about the change in board leadership. Board trustees Pauline Lieu, Tom Brennan, Leslie Williams, George Warren, and Ken Antonucci could not be reached for comment.

Mayor Gary Christenson of Malden, who is not involved in the management of the school, praised its leadership.

“We have a good working relationship with Mystic Valley Regional Charter School, and I don’t expect a change in leadership to impact that,’’ he said.

Over the years, Mystic Valley has been ranked as one of the top schools in the state by Newsweek, The Washington Post, and US News & World Report. According to the Department of Elementary and Secondary Education, 91 percent of the school’s 2015 graduation class planned to attend a four-year college and another 6 percent said they would attend a two-year college.

While the school is slated to begin its expansion in 2017, little about the Board of Trustees is made public on its website, save for the names of the current members. The minutes and agendas of Board of Trustee meetings are not posted on the website, nor are the new bylaws. The state’s Open Meeting Law requires the school to post its meeting notice and agenda 48 hours in advance of a public meeting. Notices may be posted on a bulletin board, in a loose-leaf binder, or on an electronic display. The state requires the school to keep permanent records of its open meeting minutes.

Kinnon and Gately did not respond to requests from the Globe to provide the school’s new bylaws, and copies of recent minutes and agendas from trustee meetings.

In a copy of the new bylaws obtained from the Department of Elementary and Secondary Education, the board agreed to limit trustees to a maximum of four five-year renewable terms. In addition, the new bylaws limit the board’s overall management scope, specifically barring trustees from overseeing day-to-day operations unless there are “extenuating circumstances.’’

Department of Elementary and Secondary Education spokeswoman Jacqueline Reis declined to comment on the change in leadership at Mystic Valley.

Steven A. Rosenberg can be reached at srosenberg@ globe.com.