More than six months after launching a national search, officials at the Science Museum of Minnesota have named the organization’s 16th president and CEO.

The museum’s board of trustees announced Thursday that Alison Rempel Brown, 57, would replace interim President John Stanoch in May. Brown, a Bay Area native, most recently served as chief of staff at the California Academy of Sciences in San Francisco — an institution housing the world’s only all-in-one aquarium, planetarium and natural history museum.

She will be the first woman to head the Science Museum, one of the region’s premier education centers and tourist attractions.

During her 17-year tenure in San Francisco, Brown acted as chief finance and operations officer, overseeing a transition period that involved an extensive rebuilding project and the opening of a new facility in Golden Gate Park. Former colleagues credit Brown’s leadership with doubling attendance and boosting the Academy’s membership.

Brown said she was drawn to Minnesota because of the museum’s national reputation, friendly staff and service-oriented board that seemed to be aligned with her mission of science and education. It was “a perfect fit,” she said.

“[The board] understood that this is not a theme park,” Brown said. “They really cared about the institution that’s been around since 1907 and wanted to make certain it retained a vibrant, excellent reputation within the Twin Cities, nationally and internationally.”

When she takes the helm this spring, one of Brown’s first priorities will be to secure funding from the Legislature to replace the museum’s roof. The museum, nestled in the downtown St. Paul bluffs overlooking the Mississippi River, was rebuilt in 1999 with what officials called a major design flaw that caused water damage costing millions.

The 370,000-square-foot building, with its convertible-dome Omnitheater, attracts more than a million visitors a year. The nonprofit has an annual budget of about $40 million.

Board Chairwoman Andrea Walsh said the search committee, made up of eight board members, unanimously chose Brown because of her experience and people skills. She was also articulate about using the opportunity to make physical repairs as a chance to re-examine the guest experience, Walsh said.

“She clearly is a seasoned leader who understands the importance of getting to know the people within your organization and getting to know the community … to build a great institution,” she said.

In the long term, Brown wants to help expand and engage the museum’s audience while remaining relevant in a changing culture.

“We can’t present mere facts,” she said, adding that interactive exhibits are the best ways to remain authentic but have fun. “It’s a shared experience … that you can’t get by sitting around a couch — and I think that’s what we’re competing with.”

Brown will fill the vacancy left by former President Eric Jolly, who left last summer after 11 years to head Minnesota Philanthropy Partners, a network of St. Paul-based foundations.

When she moves to Minnesota with her husband, an artist, she will have plenty of company. Brown, who spent a winter here in the 1980s as a programmer, has family ties to Minnesota. Her grandparents met at Carleton College in the 1920s, and many relatives have since attended the school, she said.

Brown received her master’s in business administration from the University of Chicago’s Booth School of Business, where her area of concentration was nonprofit and government organizations. She holds a bachelor’s degree in economics with an emphasis in mathematics from Pomona College in Claremont, Calif.

In 2008, the San Francisco Business Times named Brown as Chief Financial Officer of the Year for guiding the academy through massive structural changes. For the next three consecutive years, the paper recognized Brown as one of the Bay Area’s most influential women in business.

During her newest challenge, Brown said she hopes to observe in order to best learn.

“As I like to say, I have two ears and one mouth, and I should use them in that proportion.”