State Education Commissioner John King is stepping down to join the U.S. Education Department after three-and-a-half years leading the state’s turbulent and divisive transition to tough new learning standards and teacher evaluations.

King has served as the state’s top education official since 2011, during which time he managed the rollout of the Common Core standards and a new teacher-rating system that for the first time factored in student test scores. Both policies were backed by the federal government and many school-reform advocates, but they enraged many parents who saw their children’s test scores plummet and educators who felt ill-prepared for the sweeping changes. Even as his critics, including the state teachers union, called for his ouster, King defended the initiatives as necessary reforms.

King will step down at the end of the year and join the Obama administration as a senior advisor to Education Secretary Arne Duncan.

“I’m humbled and honored to have the chance to work with President Obama and Secretary Duncan,” King said in a statement. “We have accomplished great things for New York’s students. As a kid whose life was saved by the incredible teachers I had in public schools in Brooklyn, I’m proud to have served my fellow New Yorkers.”

King, the state’s first African-American and Puerto Rican education commissioner, was 36 when he was appointed to replace David Steiner, under whom he had been a top deputy.

He moved swiftly to put the new learning standards into practice after the state adopted the them in 2010, introducing Common Core tests ahead of most states and before many schools had updated their textbooks. The first round of Common Core tests last year caused students’ scores to plummet, and when the changes drew inevitable backlash, King proved less savvy at managing criticism. Last fall, he called off a series of public meetings about the new standards after the first one proved contentious, earning scorn from parents and the state teachers union.

“The disconnect between the commissioner’s vision and what parents, educators and students want for their public education system became so great, NYSUT voted ‘no confidence’ in Commissioner King last spring and called for his resignation,” the New York State United Teachers said in a statement Wednesday, adding that it hoped King “has learned from his stormy tenure in New York.”

As the criticism mounted, King was also losing crucial allies across the state. Gov. Andrew Cuomo backed legislation to untie student test scores from teacher evaluations for two years, something that King had steadfastly refused to support. And the de Blasio administration in New York City has proved a less willing partner than the Bloomberg administration, sparring with the state over its plans to intervene in struggling schools.

King has also criticized the city’s education department at points, especially for its enrollment policies that he said too often left schools with concentrations of high-needs students. While his strong support of charter schools contrasts with city schools Chancellor Carmen Fariña’s mixed views on charters, she has publicly backed King and the Common Core.

“It has been a privilege to work so closely with Commissioner King as we move our school system forward,” Fariña said in a statement. “I congratulate him on his new role and look forward to our continued collaboration.”

King’s departure leaves a leadership void at the state education department at a time when its direction is less certain. The Race to the Top education grants created by the Obama administration pumped millions into the state education budget during King’s tenure, empowering him to push for sweeping policy changes, but that funding is now running out.

He is the second top state education official to take a job at the federal education department in less than a year: Amy McIntosh, who oversaw teacher evaluations as a senior fellow at the Board of Regent’s Research Fund, is now a deputy assistant secretary. Two of the state’s deputy commissioners, Elizabeth Berlin and Ken Wagner, will manage the department after King’s departure, officials said, and a subcommittee of the state’s Board of Regents will launch a search for a permanent replacement.

The news of King’s move, which became public on Wednesday evening, appeared to catch some state education officials off guard. Sources said that King had not informed staff about the move and that an announcement was planned for next week’s Board of Regents meeting.

But King has been a favorite for high-profile positions outside of New York before. In 2010, when he was serving as deputy commissioner, King turned down an offer to take over as superintendent of Newark’s schools. King had also been tapped to join the federal education department before, an offer he also turned down because his tenure in Albany was young, sources said.

Before serving as state commissioner, King served as a managing director at Uncommon Schools, a charter school network and founded the high-performing Roxbury Preparatory Charter School in Boston.

King has deep roots in Brooklyn, where his father was the borough’s first African-American school principal. King attended P.S. 276 in Canarsie and Mark Twain Junior High in Coney Island, and he credited teachers there for inspiring him after both of his parents died before his 13th birthday.

“As a teacher, principal and policymaker, my goal is and has always been to give every student what Mr. Osterweil gave me — a classroom where they feel supported and inspired and challenged,” King said in April.