Richard A. Carranza will resign as chancellor of New York City’s public school system, the nation’s largest, in March, city officials announced Friday. The abrupt move comes after disagreements between Mayor Bill de Blasio and Mr. Carranza over school desegregation policy reached a breaking point in recent weeks.

Mr. Carranza, 54, is leaving one of the most influential education jobs in America about three years after he was appointed, and just 10 months before the end of Mr. de Blasio’s second and final term.

He will be replaced by Meisha Porter, a longtime city educator and current Bronx superintendent who will become the first Black woman to lead the sprawling system, which has over 1 million students and 1,800 schools. Ms. Porter, 47, will take over as chancellor on March 15.

“I know the pandemic has not been easy for you, or for any New Yorker. And make no mistake: I am a New Yorker. While not by birth, by choice,” Mr. Carranza said during a news conference on Friday, fighting back tears. “A New Yorker who has lost 11 family and close childhood friends to this pandemic. And a New Yorker who quite frankly needs to take time to grieve.”

Mr. Carranza did not have a signature initiative, and he was not able to usher through major desegregation policy, despite his bold declarations. But the chancellor did play a major role in ensuring that New York City was the first large district in the country to fully reopen schools last September and October. Mr. Carranza has maintained better relations with some teachers’ union officials than Mr. de Blasio, and he helped negotiate with the city’s powerful unions to reopen classrooms.

Mr. Carranza’s announcement follows years of tension between the chancellor and the mayor involving who had the final say over major education decisions. The chancellor and other senior education officials sometimes felt that their expertise was overruled or disregarded by Mr. de Blasio, who runs the school district under mayoral control.

The two men repeatedly clashed over school desegregation policy in particular.

Mr. Carranza vowed from his first day as chancellor to tackle entrenched segregation in the city’s schools, while the mayor has largely avoided even using the word. New York is home to one of the most segregated public school districts in the nation, a trend that has worsened over the last few decades as the city has introduced more selective admissions policies for elementary, middle and high school.

It became clear several months into Mr. Carranza’s tenure that the mayor and chancellor had fundamentally different approaches to the problem, particularly when it came to selective admissions policies and gifted and talented programs.

The long-simmering issues came to a head earlier this month, during one heated conversation between Mr. Carranza and Mr. de Blasio over the future of gifted and talented classes, according to several sources with direct knowledge of that conversation. Mr. Carranza drafted a resignation letter after that meeting, but did not immediately quit.

At issue was whether the city should continue to sort 4-year-olds into gifted and talented classes through a selective admissions process. Mr. de Blasio had said that the city would continue to offer an admissions exam for toddlers this year, then announce a new admissions system before he leaves office in January.

Mr. Carranza has consistently said he wanted the test abandoned altogether, and that the city’s gifted program is fundamentally flawed and unfair. White and Asian-American students make up about 75 percent of the city’s gifted offerings, whereas Black and Latino children make up about 70 percent of the overall district.

The city will not give the test this year, but only because an education panel that typically acts as a rubber stamp for City Hall took the extremely rare step of rejecting Mr. de Blasio’s plan to offer it. The city will instead create a lottery system for young children who are recommended by their pre-Kindergarten teachers or who sit for a short interview.

Even that stopgap measure has been criticized by integration activists who say it will do little to diversify the programs.

Mr. Carranza is the second senior cabinet member to leave Mr. de Blasio’s administration during the pandemic; health commissioner Dr. Oxiris Barbot resigned last August. She, too, feuded with the mayor over his decision-making process and said she felt increasingly marginalized.

Mr. Carranza, who led the Houston school district during Hurricane Harvey and previously ran San Francisco’s public schools, was Mr. de Blasio’s second choice for a job that some education experts consider the second-most important in the country, after the federal education secretary.

He was hired in a hurry, after the mayor’s first choice, Alberto M. Carvalho, the superintendent in Miami, turned down the job on national television. Mr. Carranza was appointed a few days later.

From his first news conference as chancellor, it was clear that he was much more willing to speak forcefully about school segregation than his boss. And a few months after he took office, it appeared that his oratory might translate into action. In June 2018, the mayor and chancellor announced a plan to get rid of the selective admissions exam that dictates entry into the city’s elite high schools, including Stuyvesant High School and The Bronx High School of Science.

Black and Latino students are extremely underrepresented in those schools, and low-income Asian-American children are overrepresented. Some Asian-American politicians and families were insulted that they were not consulted about the plan, and many took offense to Mr. Carranza’s clumsy defense of the proposal. “I just don’t buy into the narrative that any one ethnic group owns admission to these schools,” he said shortly after it was announced.

A major backlash to the plan, led by Asian-Americans, quickly killed the mayor and chancellor’s hopes of replacing the specialized school admissions exam. The parents who fought to keep the exam in place have since become Mr. Carranza’s harshest and most consistent critics. Before the pandemic, a group of families followed the chancellor to all of his public appearances, chanting “Fire Carranza!” and accusing him of bias against their children.

Mr. de Blasio’s administration has not created major new integration policies since that humiliating political defeat in 2018. The pandemic, however, forced the mayor to announce some changes to selective admissions policies late last year, including abolishing a rule that gave students in some of the city’s wealthiest neighborhoods first dibs at selective high schools there. Mr. Carranza and his senior aides had been pushing the mayor for years to get rid of that geographic preference, which applied to students living on the Upper East Side, the West Village and Tribeca.

Mr. Carranza’s language about integration has often directly contradicted Mr. de Blasio’s stance, which has consistently irritated the mayor and his press team. The chancellor has a habit of publicly contradicting the mayor on a range of issues.

Just a few days after he started on the job, Mr. Carranza called the idea behind the mayor’s nearly $800 million school improvement program, called Renewal, “fuzzy.” The chancellor later had to defend the program, even after the city canceled it after disappointing results. That trend has continued to the final days of Mr. Carranza’s tenure.

Earlier this week, the chancellor encouraged families to refuse standardized testing this year, after President Biden’s administration said states would have to give exams amid the pandemic. Mr. Carranza’s stance directly contradicted the mayor’s message on test refusal.

Though Mr. Carranza had hoped to focus on integration policy, he has spent the last year overseeing the most consequential school reopening effort in the country.

The chancellor and mayor were aligned in pushing to open New York City classrooms last fall, after a rushed experiment in remote learning.

Still, the reopening effort has been extraordinarily complex and fraught with logistical issues.The mayor closed all schools in November as virus cases rose, then reopened only elementary schools in December. Middle school students returned to their classrooms earlier this week. It is not yet clear if high school students will return to school buildings before the fall, though Ms. Porter said during Friday’s news conference that the city was “ready to go” on reopening high schools.

“We have stabilized the system in a way no one thought possible,” Mr. Carranza said. “The light is at the end of the tunnel.”

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