A Bronx assistant principal will take over Brooklyn’s troubled Boys and Girls High School, officials said Monday, over the objections of some staffers and alumni who had rallied behind a different candidate.

Grecian Harrison, an assistant principal at Alfred E. Smith Career and Technical Education High School for the past 13 years, will become interim-acting principal of Boys and Girls, which has emerged as the face of Mayor Bill de Blasio’s high-stakes effort to revamp the city’s lowest performing schools. The school’s previous principal decided abruptly last month to leave less than two years after the city recruited him for the job.

Officials also announced Monday that Automotive High School, another long-struggling Brooklyn institution, will get a new principal: Kevin Bryant. Bryant currently runs Frances Perkins Academy, a tiny school that shares a building with Automotive but boasts a far higher graduation rate.

Automotive has faced setbacks similar to Boys and Girls: The state has labeled both schools “out of time” to make drastic improvements, and Automotive’s principal also recently left the flailing school. Both schools are part of de Blasio’s “Renewal” improvement program, which infuses low-performing schools with extra resources and classroom support.

“These are the right principals to continue the hard work of turning a school around,” Chancellor Carmen Fariña said in a statement. “I know they’ll be strong instructional leaders and support students, teachers, and families.”

The decision at Boys and Girls comes as a major disappointment to some staffers and alumni who had thrown their support behind Allison Farrington, the popular principal of a small high school housed inside Boys and Girls’ campus. Last month, representatives of Boys and Girls’ teachers, parents, and alumni signed a letter to Fariña backing Farrington and two other candidates — but not Harrison — and asking for a greater role in the selection process.

Beyond allowing them to submit their recommendations, the selection process had given those groups “no real voice in determining who the next principal will be for this historic educational institution,” the June 27 letter said. Ultimately, the city rejected their recommendations and opted for Harrison, who most recently oversaw the ninth grade, social studies department, and physical education at Smith.

On Saturday, Brooklyn City Councilman Robert Cornegy wrote Fariña asking her to postpone any announcement until she had reconsidered “the community’s request” to appoint Farrington. He added: “I believe it is grossly unfair to the BGHS community to select an instructional leader from outside the community,” according to the letter, which was obtained by Chalkbeat. (Cornegy’s office did not immediately respond to a request for comment, but he has previously said he would be “pissed off” if he was not able to participate in the selection process.)

The education department’s hiring rules authorize superintendents to choose interim-acting principals, though the chancellor must approve them. After that, a committee of parents, students, and union representatives must have an opportunity to interview at least three principal candidates before the superintendent makes a final decision. In the case of Boys and Girls and Automotive, the city entered into an agreement with the teachers and principals unions that requires principal candidates at those schools to apply to an additional committee as well.

David Bloomfield, an education professor at Brooklyn College and the CUNY Grad Center, said it appeared the city had adhered to the rules and the agreement in appointing Harrison as an interim-acting principal. However, he said that by not discussing the decision ahead of time with people at the school, the department may have made it harder for Harrison to unify the school community around her.

“By acting in what appears to be a high-handed manner,” he said, “they are hobbling their own candidate.”

Education department spokeswoman Devora Kaye said Superintendent Michael Alcoff met with the Boys and Girls community before making his selection “to discuss how seriously he was taking this process,” and added that he will continue to meet with them.

Once the premier high school in Bedford-Stuyvesant, Boys and Girls has declined precipitously in recent years. Since 2010, its enrollment has plummeted by 85 percent, and its graduation rate remains 20 points below the city average.

Its previous principal, Michael Wiltshire, raised the school’s on-time graduation rate 8 points, to 50 percent, and sharply reduced the number of suspensions it gave out. Harrison now faces the daunting task of maintaining those gains while stabilizing the high-profile school, which shed three-quarters of its teachers last year.

“As a proud Brooklyn and Bed-Stuy native, I am committed to building on the progress and continuing to improve student achievement at Boys and Girls High School,” she said in a statement released by the education department.

Bryant faces a similar challenge. Automotive’s four-year graduation rate was even lower than Boys and Girls’ last year: 46 percent, compared to the city’s 70 percent average. It now serves just 380 students — only slightly more than Boys and Girls’ 340 — at a time when Fariña is closing or consolidating very small schools.

However, in a slight glimmer of hope, the state recently removed the school from its list of “persistently struggling” schools.

“I look forward to working to strengthen instruction, increase student support, and improve outcomes at Automotive High School,” Bryant said in a statement.

Frances Perkins’ graduation rate climbed from 46 to 73 percent under Bryant, officials said. His new role will be “master ambassador principal,” meaning he will continue to oversee some aspects of Frances Perkins even as he tries to revamp Automotive.

Wiltshire, the former Boys and Girls principal, held a similar role but struggled to simultaneously run two schools. In leaving Boys and Girls, he has returned to overseeing just one school.