Brentwood schools Superintendent Levi McIntyre is stepping down as leader of Long Island’s largest school district, in the sprawling Suffolk County community still reeling from recent gang violence, officials confirmed Friday.

McIntyre, 69, is expected to leave the post June 30, both school board president Elizabeth Mercado and Assemb. Phil Ramos (D-Brentwood) said.

His leave-taking will come a year before expiration of his three-year contract, signed in March 2015, that initially paid $206,000 annually.

McIntyre could not be reached for comment Friday.

“There was an amicable separation between the current board and the superintendent,” Mercado said.

She said the board will seek an interim superintendent and declined to comment further.

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Tuesday’s school board elections mean change for the panel — both immediately and in July — with three new trustees winning seats.

Maria Gonzalez-Prescod and Simone Holder-Daniel each were elected to a three-year term and will take their seats in July. Candidate Julia Burgos, who won a one-year term that fills out time remaining on the term of a board member who died, was sworn in this week. Burgos declined to comment Friday.

McIntyre, a longtime Brentwood resident, worked for years in the nearby Longwood school system and came out of retirement to take the Brentwood job.

He has led the Brentwood district, which has an enrollment of nearly 20,000 students, at a time when the community and neighboring Central Islip have been rocked by gang violence that law enforcement authorities have attributed to the brutal MS-13 group.

The death toll in the past year has risen to 11, including the slayings of Brentwood High School students Nisa Mickens, 15, who was found killed along with her friend Kayla Cuevas, 16, in September.

School officials have faced criticism over security in district schools.

McIntyre ordered strengthened security measures, including mandates that students and staff wear photo identification inside school buildings at all times and the use of metal detectors and wands to randomly search students.

Ramos, who has been critical of the district’s leadership, said McIntyre “made a lot of bad decisions” and misdirected resources. The assemblyman also said that school officials looked to hire family and friends for positions within the district.

The announcement of McIntyre’s departure represents “the dawn of a new day in the Brentwood school district,” Ramos said.

The superintendent received his bachelor’s and master’s degrees from Indiana University and his doctorate from the University of South Florida. He was born and grew up in Jamaica, where his father worked in a sugar cane factory.

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In 2012, McIntyre was named “Administrator of the Year” by the Western Suffolk Counselors Association.