Eric J. Smith, the nationally renowned educator who took command of the Anne Arundel school system in 2002 and brought three years of academic prosperity and political tumult, announced yesterday that he will resign to take a job at Harvard University.

He announced his exit less than two months after the release of an audit that found deep faults in the school system's human resources department, including allegations of unorthodox hiring bonuses and undeserved pay raises. While the report seemed far removed from the core of Smith's academic mission, it set off a round of public acrimony between Smith and members of the school board. The rift, in Smith's mind, proved irreparable.

The disputes "have resulted in considerable distraction from the important work that I was brought here to do and that I love doing," Smith said in a statement released at the end of the workday.

Smith said he accepted a position in "leadership development" at the Harvard Graduate School of Education. A spokeswoman for Harvard said she had no information on Smith's hire.

Smith, who had nine months remaining on his four-year contract, said he informed school board President Konrad M. Wayson of his intentions Aug. 23 and "they had an opportunity to come back and respond to me." Smith said no response came. But board member Eugene Peterson said the group did reply, through an attorney, that it expected Smith to complete his contract.

Wayson said he learned of Smith's decision to leave, effective the day before Thanksgiving, in a 5 o'clock telephone call -- not from Smith but from the county executive, Janet S. Owens. "I knew we were working through issues, but, yeah, I was surprised," Wayson said.

Smith will leave the 75,000-student Anne Arundel school system in better shape academically than when he arrived. Participation in college-level Advanced Placement courses has more than doubled in Anne Arundel over the past three years, under Smith's philosophy of expanding access to demanding coursework. Students improved across the board on the 2005 Maryland School Assessment test. Smith has introduced the prestigious International Baccalaureate program to Anne Arundel high schools and overhauled class schedules so students could take a greater variety of courses.

"A lot of [my] classes didn't exist when I was a freshman," said Pallas Snider, a senior at Severna Park High School and the student member of the school board. "I have benefited from a lot of changes to come into the school system, personally."

Just this month, leaders of both the county PTA and an influential community advisory group had publicly endorsed Smith and had urged the school board to renew his contract next summer.

"He's doing what we asked him to do," said Debbie Ritchie, the countywide PTA president, who cited particular satisfaction with Smith's having placed a scattershot school system on a common plan of lessons and books. "He brought it all together and he made it more a continuum," Ritchie said.

But neither she nor others in the school system's inner circle expressed much surprise at Smith's announcement. Questions of fidelity had loomed since spring 2004, when Smith emerged and then faded as a candidate to lead the much-larger Miami-Dade school system in Florida.

Smith, 55, came to Anne Arundel in summer 2002 from Charlotte, where he had earned and cultivated a national reputation for narrowing the achievement gap between black and white students. Anne Arundel was his fourth superintendent's post.

After beginning his career as a math and science teacher in Orlando in 1972, he moved up the ranks and, by 1990, had become superintendent in Danville, Va. He took over the top job in Newport News, Va., in 1992 and in Charlotte four years later.

He came to Anne Arundel with an unprecedented package of $300,000 in annual salary and benefits. Within weeks, the hard-charging Smith had ranked and sorted the schools, axed unwanted programs and launched others to replace them.

But Smith eventually clashed with the school board and the teachers union at various times, usually over money. Teachers perennially accused him of increasing the workload without adequately raising their pay. Last month, the teachers union released a survey of teachers showing near-universal disfavor in such areas as cooperation and trust.

Sheila Finlayson, the union president, said of Smith's departure, "I think he's choosing to not deal with the issues at hand."

The audit of Smith's human resources department, released in mid-July, fractured the relationship between the superintendent and the board. It led several board members to publicly question their trust in Smith, even as the superintendent raced to adopt some of the auditor's recommendations. Among the embarrassments was a last-minute scramble to verify criminal background checks on thousands of school-system employees, set off by an audit finding that some files lacked such proof, and the revelation of an earlier audit, released in 2002, that had reached some of the same findings about the department.

There were also questionable sums paid as pre-employment bonuses to top staff brought to Anne Arundel by Smith. In public comments, school board members made clear that they resented not knowing about the payments and would not permit them in the future.

In a series of interviews about the audit in recent weeks, Smith vowed reforms but also defended his particular way of doing things, indicating he would not be ruled by either the teachers or the school board.

"When I was hired here, there was no surprise about my style," Smith said in one interview. "There's a million decisions that are made over the course of the week, and I believe that the superintendent, if they're to be effective and accomplish what the board wants them to accomplish, needs to make calls."

Superintendent Eric J. Smith said disputes with the school board distracted "from the important work that I was brought here to do."