Braly had been subject to mounting investor scrutiny following a disappointing second-quarter earnings report. Despite her support from the board and WellPoint’s well-received $4.9 billion acquisition of Medicaid specialist Amerigroup, the stock’s recent poor performance fueled long-standing anxieties from major investors about Braly’s tenure. Between yesterday and when she took over in 2007, WellPoint’s stock fell 30%, badly trailing the sector and the S&P.

WellPoint is one of the largest health insurers in the U.S. by membership, covering around 33.5 million people. But that number has fallen recently (in June, membership was down 1.9% from the previous year), reflecting tumult in a fast-changing industry. It also probably didn’t help that Braly tussled with President Obama in 2010, when WellPoint drew national ire for its rate increases in California.

Braly’s sudden and fraught departure stands in contrast to the performance of another woman in health care on Fortune’s MPW list — Gail Boudreaux at UnitedHealth Group , CEO of the company’s $95 billion UnitedHealthcare business. UnitedHealth Group’s stock is up 7% this year, even as WellPoint’s declined 13%. UnitedHealth has also picked up more members than WellPoint.

Still, in a parting letter to employees, Braly sounded a confident note: “I have spoken with our board and we have agreed this is the right action for WellPoint at this time. We are in a very strong position strategically,with our recent actions positioning us well for the changes to come in health care. The company’s foundation is secure, in large measure because of the strong work and commitment of our 37,000 associates, and for that I thank you. It has been a privilege and honor to work with the terrific associates at WellPoint, and to see first-hand all the great work you do for our members. One of our great strengths is the culture we have built together, which always puts the customer first. The board and I feel, though, that the company will benefit from getting a fresh perspective on ways we can improve execution across the company.”