D.C. Public Schools Chancellor Kaya Henderson will step down from her position in September. Mayor Muriel E. Bowser (D) shared the news in a statement Wednesday. (WUSA9)

D.C. Public Schools Chancellor Kaya Henderson, who built a national reputation for shepherding a troubled school district through rapid improvements, announced Wednesday that she will step down from her post in the fall.

Mayor Muriel E. Bowser (D), who said she did not ask Henderson to resign, immediately tapped John Davis, the school system’s chief of schools, to serve as interim chancellor beginning Oct. 1. A national search for a permanent chancellor will begin later this year, but a replacement likely won’t start until the 2016-2017 school year concludes.

Henderson was preceded by Michelle Rhee, who drew attention — and scrutiny — for her combative approach to improving the city’s schools. In a combined 10 years leading the city’s schools between them, Rhee and Henderson’s experiment in school reform became a national bellwether for urban schools.

Bowser said that the city’s school-reform efforts will not slow under the next chancellor.

“While we have made progress, no one should think that we are stopping,” Bowser said. “We want to send a strong signal that we’re putting a foot even further down on the gas when it comes to public school reform.”

Kaya Henderson, chancellor of D.C. Public Schools, chats with students as they enter Eastern High School in this file photo from the first day of school on Monday, Aug. 25, 2014. (Amanda Voisard/For The Washington Post)

Henderson had long said she planned to stay at the helm of the city school system until at least 2017. But in an interview Wednesday, she said that leaving in September — a “slow time” for the school system, after the new school year begins — feels right.

She has led the school system for more than five years, far longer than the average three-year tenure of school superintendents in big cities. And she said leading the nearly 50,000-student system has been strenuous; she plans to relax and spend time with her family for at least six months before considering other offers in the education field.

“This is dog years on your life,” Henderson said of her job. “Leadership is about knowing when to pass the baton. I know that there are other people that can pick it up and run with it.”

Henderson’s unexpected departure comes as the city is experiencing an influx of wealth and new residents, and more parents are choosing D.C. Public Schools. During Henderson’s five-year tenure, test scores have improved, schools have beefed up academic and extracurricular offerings and the system — once considered among the most dysfunctional in the nation — has been hailed by President Obama as an example of promising reform.

“What she’s done here is not only just improve the academic outcomes, she’s managed to stabilize the system,” said Michael Casserly, executive director of the Council of the Great City Schools, a coalition of large school districts. “She’s given the city a sense of optimism and hope that its public school system can be what they want it to be.”

Despite the widespread accolades, the school system has not been without its troubles in recent years, with many questioning whether the city’s approach to fixing its schools has benefited its neediest children. Although overall scores on national standardized tests have been among the fastest-rising in the nation, there are still stark achievement gaps separating white and black students and the wealthy and poor.

Aside from academics, there also have been controversies involving the school system’s handling of its food-service contract and, more recently, over the testing of lead in water at city schools.

A onetime Spanish teacher and Teach for America executive, Henderson arrived at D.C. Public Schools in 2007 as a deputy to Rhee, the then-chancellor who had an unapologetically combative approach to reform and an antagonistic relationship with the city’s teachers union.

Rhee abruptly closed more than 20 schools. And under her leadership, the city’s school system became among the first in the nation to judge teachers and principals — and fire them — based in part on how their students performed on standardized tests.

When Rhee resigned after then-Mayor Adrian M. Fenty lost his reelection bid, many wondered whether her reform efforts would be abandoned. But Henderson continued them, albeit with a softer touch that ignited fewer public firestorms.

Now Henderson says that D.C. Public Schools is staffed with a deep bench of talented people who share her philosophy, and she doesn’t believe her departure will result in significant change.

“I set about to build an institution where one person leaving wouldn’t matter anymore,” Henderson said. “I have a team that is raring and ready to go, and I think just because people don’t know them doesn’t mean they’re not capable. People didn’t know me, either.”

In an interview on Oct. 2015, D.C. Public Schools Chancellor Kaya Henderson talks about the challenges of turning around the troubled school district. (DC Office of Cable Television)

Davis, the incoming interim leader, is a former Baltimore teacher and administrator who, like Henderson, came to the District in 2007 to work with Rhee.

While Bowser lauded the chancellor Wednesday, she did not definitively say she would hire a new chancellor whose leadership approach mirrors Henderson’s.

“Part of searching for a new chancellor will be taking the pulse of the community, getting feedback from stakeholders and moving forward,” Bowser said.

Henderson has had a rocky relationship with the Washington Teachers’ Union. The teachers’ contract expired in 2012 and has yet to be renewed, with each side blaming the other for stalled negotiations. Elizabeth Davis, the head of the WTU, said she hopes to finish contract negotiations before Henderson leaves.

Under Henderson’s leadership, the city became one of the first big school districts to embrace the Common Core, overhauling its curriculum in math and reading. She has pushed to change the trajectory for poor and minority children by extending the school day and year at some schools, by opening a school meant to prepare black males for college, by offering new career-education academies and by creating a summer study-abroad program.

The school system has been among the nation’s fastest gainers on the National Assessment for Educational Progress, often called the Nation’s Report Card, although achievement gaps are wide: Just 17 percent of black fourth-graders are proficient in reading, for example, compared with 82 percent of white fourth-graders.

Henderson has pumped millions of dollars into secondary schools, aiming to keep students in the system as they hit middle school, when they historically have chosen to leave for charters, private schools or stronger suburban systems in Maryland and Virginia. Those efforts — a key Bowser priority — have had middling success: Between fall 2015 and fall 2016, DCPS middle school enrollment dropped by nearly 400 students, while the city’s charters saw nearly equivalent growth.

Greg Rhett, a parent who lives in Ward 7 — a predominantly poor, black area east of the Anacostia River — said he has to send his daughter to a middle school in Capitol Hill to give her a challenging academic experience.

City data shows that a majority of students in Wards 7 and 8 transfer to DCPS schools outside their neighborhoods or choose charters. “There’s just a lot that is lacking east of the river,” Rhett said. “She came in, there was an achievement gap for children of color and I think that achievement gap still exists.”

But overall, DCPS’s efforts to improve and market itself have paid off. After a four-decade enrollment decline, the city’s student population has grown for the past four years.

“We are the nation’s capital, and we should have a school system that we should be proud of,” Henderson said. “That wasn’t the case before, and that is the case now, and I feel proud to be part of that.”