Just last year, the team hired Gideon Yu, former CFO of Facebook, to be its president. That hire was among a slew of notable additions made by young CEO Jed York since he took the top spot in 2010. His other moves included hiring Coach Jim Harbaugh and General Manager Trent Baalke both for the 2011 season; Harbaugh won Coach of the Year.

Herman was key in setting up the IPO for Facebook; certainly some Valley insiders will figure the disappointing offering was key in her choice to leave. It’s also notable that this move is being announced just hours before Facebook is scheduled to release its latest earnings report.

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In an internal memo sent to 49ers staff Monday evening, Yu wrote: “At Facebook, [Herman] was instrumental in setting up their financial operations and completing numerous financings, including their recent IPO. She also held positions at Hewlett-Packard and Seibel Systems… More importantly, Cipora is a huge sports fan — both of the 49ers and of the Boston Celtics. She has two wonderful children (Sarah and David) and is married to Vlado (former CFO of Yelp).”

In 2010, Jed York had publicly predicted his team would win its division and make the playoffs, much to the derision of pundits and opposing fans, but the Niners indeed came very close. The next season, his prophesy came true, thanks largely to the success of Harbaugh and quarterback Alex Smith. It was the first time the team made the postseason since 2002, nearly a decade, and this return to franchise success earned York a spot on our 40 Under 40 list this year.

Off the field, York, working with Yu, also successfully closed the financing for the team’s gargantuan new $850 million stadium, set to complete construction in 2014.

Current CFO Larry MacNeil will stay on as EVP of Development, devoting all of his time to the stadium project, and, Yu tells Fortune, to “making sure it is going to be the best sports venue in the NFL.” That’s a tall order, but with Herman, York, 10-season CFO MacNeil, and Yu—who worked at Facebook (FB), YouTube (GOOG) and Yahoo (YHOO)—all on board, the team boasts a formidable management cadre.

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“This is a dream job,” says Herman of joining the team. “After five years at Facebook, rolling up my sleeves through a lot of the formative years of the company, it was just the right transition point for me.” Herman says she will focus mostly, of course, on the completion of the stadium, but also “helping out Jed and the management team any way I can, and maybe that’s helping to extend the brand. The 49ers are a storied franchise, and there’s a lot more brand-building that can happen there.”

It was Yu who hired Herman at both Yahoo and Facebook, so this marks the third time they’ll be teaming up. “Cipora is one of the top financial executives in the business,” Yu says. “We are thrilled to have her join us.”

It’s an exciting time for Bay Area sports fans: the Niners lead their division with a record of 5-2 after beating Seattle in their division opener last Thursday. The Giants mounted a nice comeback against the St. Louis Cardinals, winning three games in a row to take the NLCS and a ticket to the World Series against Detroit. And on Thursday evening, as the Giants are battling the Tigers, Fortune will be in town, toasting Jed York and other members of the 40 Under 40 list at our annual party.