University of Washington President Mark Emmert is leaving to become president of the NCAA.

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On Monday, Mark Emmert stood up the governor.

On Tuesday, she got an urgent phone call: “It was, ‘He has 15 minutes and he must talk to you before he boards an airplane.’ I thought, ‘Oh my gosh, he’s leaving,’ ” said Gov. Chris Gregoire.

Emmert announced Tuesday that after nearly six years as president of the University of Washington, he was stepping down to take the top job at the National Collegiate Athletic Association. Emmert takes over at the NCAA in Indiana on Nov. 1.

While the timing of his announcement caught Gregoire and other state leaders by surprise, there were hints in recent months that the charismatic UW president was growing restless.

There were the battles he fought and lost with state lawmakers over higher-education funding. The blistering e-mails his wife, DeLaine, sent in frustration. The rumors that kept linking him to other job searches. And the fact that at 57, he enjoyed a national reputation and appeared poised to play a final career hand.

Emmert has been considered a rainmaker during his tenure in Seattle. One of his biggest achievements was leading an enormously successful fundraising effort that had brought in $2.68 billion by the time it ended in 2008.

He’s also been credited with recruiting top faculty, overseeing the continued success of the UW’s medical school and, most important to many alumni, helping turn around a beleaguered football program.

But Emmert seemed to lose something of his golden touch in the last couple of years. His compensation package of $906,500, which made him one of the highest-paid college presidents in the country, became a source of irritation to faculty and the public — especially as the UW was forced to cut services and eliminate some 850 staff positions due to severe state budget cutbacks.

In Olympia, lawmakers saved some of their deepest cuts for the UW. The budgets for community colleges, considered by some lawmakers as more expedient in creating jobs and turning around the economy, were largely spared.

The strain of those cuts and Emmert’s inability to win battles like gaining control over tuition-setting authority clearly took a toll on both the president and his wife. While Mark Emmert maintained his sunny demeanor, his wife was less circumspect.

“As you are very aware, the UW lost more than a quarter of its state support last year causing 100’s of jobs to be lost in your district and even more will be coming forth,” she wrote in a January e-mail to House Speaker Frank Chopp, D-Seattle.

“It had bigger cuts than any University in the country, including in California! The state is starving your district’s golden goose and yet you DON’T even mention it as a concern?!!!! … I need to know why you do not seem to care.”

DeLaine Emmert also felt uncomfortable with the scrutiny of her husband’s salary. She recently canceled their subscription to The Seattle Times after one critical column, prompting her husband to quip to a reporter that he missed getting the morning paper — but his wife did not.

And then there were the job offers. During his tenure at the UW, Emmert was courted by any number of institutions: Cornell, Vanderbilt and his former employer, the Louisiana State University System.

But sources have told The Times over recent months that he was particularly interested in two opportunities: the top jobs at the University of Southern California and at the NCAA.

When asked by The Times about the USC job earlier this year, Emmert said he’d been approached by the university but was not a candidate for the job.

Asked about the NCAA job last week, DeLaine Emmert jokingly said that she didn’t much care for living in the Midwest. When a Times reporter approached her husband on Monday to ask him about the NCAA job, Emmert said he was sorry but he was running late for an appointment and didn’t have time to chat.

Gregoire said she’d been in Seattle on Monday to dedicate the Confucius Institute.

“He was to be there and introduce me and suddenly at the last minute they said he’s had an emergency. I kept saying, ‘I don’t want to do this until I know it’s not personal.’ They finally said, ‘No, it’s not personal.’ Coming home last night I thought: What would be an emergency at a university?”

When Emmert told her what was up on Tuesday, Gregoire said she didn’t try to talk him out of leaving: “You know what, Mark, if this is what you want, despite how much this state will miss you … I want for you what you want. So I wish you the best.”

Gregoire said she credits him with many accomplishments. “I just think he put the right structure in place. When he had to make tough calls and personnel changes, he did it.”

By accepting the new job, Emmert fills a vacancy created by the death of NCAA President Myles Brand last September. Emmert will take over from interim President James Isch.

Wally Renfro, an NCAA vice president, said Emmert first interviewed for the position of president about three weeks ago and flew out for a final interview Tuesday before being offered the job.

Renfro said Emmert has signed a five-year contract with the NCAA, the governing body for collegiate sports. His major responsibility will be to meet with college presidents from across the country when athletic issues arise that need to be addressed at a national policy level.

Renfro said the NCAA, a nonprofit organization, won’t discuss the salaries of any of its employees, including Emmert. However, 2008 federal tax records indicate Brand was paid $1.72 million a year in salary and benefits.

In an e-mail to faculty and staff, Emmert said he was accepting the post with “very mixed emotions.” He said he was excited about helping shape the experiences of 400,000 youngsters at 1,200 institutions.

He said that after he and his wife came to the UW in 2004, he realized there was no other university he would want to preside over.

“DeLaine and I always have been, and always will be, Huskies for life,” he said in the e-mail. He could not be reached Tuesday for an interview.

A Washington native, Emmert earned his bachelor’s degree in political science from the UW and has both a master’s degree and a Ph.D in public administration from Syracuse University. The Emmerts have been married for more than 30 years. They have two children, Steve and Jennifer.

“Dr. Emmert has been an incredible leader at the UW,” said Herb Simon, chairman of the UW’s board of regents. “That the NCAA sought him out speaks testimony to his greatness as a leader of the university.”

Simon said the board will name an interim president sometime before Emmert leaves in the fall.

Asked about Emmert’s reasons for leaving, Simon said that he is driven by new challenges.

“The best way I could describe it was that this was a unique opportunity,” Simon said. “There is only one president of the NCAA, and it puts him on a national platform.”

Athletic Director Scott Woodward — who first worked alongside Emmert at Louisiana State University before following him to Washington — said his path and Emmert’s will now diverge.

Woodward said he loves his job and that “I plan on being here a long time.”

Bruce Balick, chair of the Faculty Senate, said Emmert’s departure was a surprise.

“He’s been a terrific president and I’m really sorry and disappointed,” Balick said. “He was a wonderful person with whom to work. Bright, articulate, sensitive, understood the university … “

Balick said he was grateful to Emmert for healing rifts with the faculty and reopening lines of communication.

“Mark recognized that faculty salaries were very important,” Balick said. “Mark was able to move forward and bring salaries up.”

Emmert also arrived at a time when the athletic program was falling apart and tried to move it “toward academic respectability as quickly as anyone could.”

Yet not all faculty members were happy with Emmert’s tenure.

Pathology professor Stephen Schwartz, who has been critical in recent months of UW Provost Phyllis Wise serving on Nike’s board, said “the whole question of the involvement of big football on this campus is scary.”

He said that as a taxpayer, he was outraged with the money “blown” on Emmert’s large salary, and said the president should be called before state lawmakers to explain his taking the new job.

Tim Mensing, president of the undergraduate student body, said he and other students will miss Emmert.

“Mark Emmert has given us six strong years of transformative leadership. He’s raised billions of dollars for us,” Mensing said. “We are happy to have had the time that we did with him, and we wish him all the best in the future.”

Staff reporters Andrew Garber, Sanjay Bhatt, Bob Condotta and Bud Withers and news researcher Gene Balk contributed to this report. Nick Perry: 206-515-5639 or nperry@seattletimes.com