Tossing another challenge onto a transit system already in upheaval, BART General Manager Grace Crunican abruptly announced Thursday that she is retiring, saying she’s been at the job longer than her predecessor and that new leadership would be good.

Her announcement at the BART Board of Directors meeting apparently took all eight of those present by surprise.

It comes as BART confronts a host of challenges, including a $25 million-a-year fare-evasion problem, aging infrastructure and trains, and growing customer frustration with crime, homeless riders and cleanliness across the transit system. Last week, BART’s police chief announced he will retire in May — and this week, the entire department went into “emergency staffing” to crack down on crime and “quality of life” issues on BART.

Crunican said her last day will be July 6, a few days after she turns 64. She has run BART for seven years.

“Everyone has to retire sometime,” Crunican told The Chronicle. “It’s a tough job, but it’s in really good hands right now. There is a good crop of leaders in place.”

She said her proudest accomplishment has been “doing a lot to secure the future of the agency,” which involved shepherding in the new, but delayed, fleet of railcars. She also said she was proud of improving labor relations, overseeing the addition of a customer trip-planning app, and overseeing billions of dollars in improvements that are either scheduled or in process for the train-control system, power system and other parts of the system.

And now, she said, “It will be good to get a fresh set of eyes in this seat.”

BART’s directors betrayed no knowledge that Crunican’s news was coming during their regular meeting on Thursday. After she made her announcement, there was a short pause before the board gave her a standing ovation. They lauded Crunican for her work in improving the rail fleet and addressing safety.

“It will be difficult to fill her shoes,” Director Debora Allen of Contra Costa County told The Chronicle. “She is a strong, direct leader. There are so many moving parts, many hidden agendas and political agendas, and I think she did a great job of balancing all the interests involved here. But I also understand that people get tired. Maybe that was just the case here.”

“The dividends are paying off in the renewal of the system,” said Director Robert Raburn, who represents Oakland.

However, some critics pointed out that Crunican is leaving at a tumultuous time for BART, a backbone transit system for the Bay Area with a $2.3 billion budget and 425,000 daily riders. A survey presented to the board in January showed that customer satisfaction plunged to 56 percent last year, down from 69 percent three years ago despite the agency’s efforts to fix old machinery, improve safety and clean its stations.

A memo issued by Police Chief Carlos Rojas and obtained by The Chronicle ordered the entire department into “emergency staffing” to address fare-jumping, “quality of life issues and crime on BART,” starting Monday. Complaints have risen in recent months about homeless people on the trains. On Thursday, NBC TV Channel 11 released a recording of what it said was a BART officer telling a rider it would be “a waste of resources” for the rider to file a report that he’d been robbed at gunpoint at a station.

State Sen. Steve Glazer, D-Orinda, a frequent critic of BART, acknowledged that leading the agency is difficult and demanding. But he was critical of its performance.

“I would say there has been great dysfunction in the agency over the past 10 years,” he said. “There needs to be accountability for that at every level, from the general manager to the board. And it has not been a very good record.”

For everything Crunican did to improve BART, she also contributed to its ongoing problems, Glazer said.

“While she made sure all BART trains had working security cameras, we still experience great security concerns,” he said. “She found money to buy new BART cars, but their acquisition is years behind schedule — years.”

Glazer also cited problems with excessive employee overtime, a fine for a BART campaign violation in the Measure RR infrastructure bond election, and two 2013 strikes that shut down the system, inconveniencing hundreds of thousands of BART commuters.

“These are hard points of analysis,” he said, “but they are accurate.”

Opinions were split among BART riders as the news rippled through the railcars.

“Good. Perhaps they’ll hire somebody that can make some changes,” Mike Nash, 69, said at Civic Center Station as he prepared to board an Antioch-bound train. “It’s time for BART to turn over a new leaf, to do something better than what they’ve been doing. Maybe a shakeup is what they need.”

A more forgiving tack came from Mike Davis, who gave no age but was middle-aged and waiting at the same station for a Pleasanton-bound train.

“I don’t think she was doing a bad job,” he said. “Maybe she was stressed out about the job. There’s a lot to be stressed about.”

The board will now be tasked with picking Crunican’s replacement. On Thursday, she suggested Assistant General Manager Robert Powers.

Crunican has served as general manager since August 2011. She came to the department from the Seattle Department of Transportation, and she succeeded Dorothy Dugger, who ran BART for four years as the system’s first female general manager.

Crunican was hired as BART’s general manager at a time of major unrest at the transit agency.

Dugger had just been fired by the board on a sharply split vote, and the agency was under attack for two shootings by BART police — including the incendiary killing of Oscar Grant at Fruitvale Station in 2009 — and for shutting down cell phone service in an attempt to stop a protest against BART police.

But the new general manager promised change at BART and said she relished the challenge. From the start, Crunican developed a reputation as a straight shooter. During her job interview, former Director Lynette Sweet said, she told directors what they were doing wrong and that they needed to focus on the basics.

“She told us off,” Sweet said in a 2011 interview. “She told us what we weren’t doing as a board, why we needed to do things differently, and went through a whole litany of reasons.”

Crunican arrived about a year after leaving a job as head of Seattle’s Transportation Department. She’d resigned after a failure to keep the city’s roads open during a major snowstorm made her a political liability.

Chronicle staff writer Erin Allday contributed to this report.

Gwendolyn Wu, Kevin Fagan and Michael Cabanatuan are San Francisco Chronicle staff writers. Email: gwendolyn.wu@sfchronicle.com, kfagan@sfchronicle.com, mcabanatuan@sfchronicle.com Twitter: @gwendolynawu, @KevinChron, @ctaun