Flagstar Bancorp, Inc. operates as the holding company for Flagstar Bank, a federally chartered stock savings bank. It is the largest publicly traded savings bank in Michigan with assets of over $16 billion in 2016. Flagstar is also a leading mortgage lender and a national leader in the wholesale mortgage business.

Flagstar was founded as a federal savings bank in 1987 under the name First Security Savings Bank. The bank's chairman was Thomas J. Hammond. The initial branch focused on funding regional retail and wholesale mortgage operations. In 1993, FSSB Holding Corporation was established. Security Savings Bank, based in Jackson, Michigan, was purchased in 1994. The company changed its name to Flagstar Bank in 1996. Flagstar Bancorp went public in 1997. In 2001, it moved its stock listing from the NASDAQ to the New York Stock Exchange. By 2009, the bank had 179 branches. Flagstar was affected by the housing-led recession of 2007, and the bank recorded losses from 2008 until the second quarter of 2012. The company raised $1.6 billion in new capital with investments from MP Thrift Investments L.P., the Treasury Department's Troubled Asset Relief Program (TARP), and public offerings. Flagstar effected 1:10 reverse stock splits in 2010 and 2012 to maintain its New York Stock Exchange listing. The U.S. Department of Treasury sold its preferred stock of Flagstar to private investors in 2013.

Flagstar reached settlements in several cases to move past the legacy issues that arose through its mortgage operations. In May 2013, Flagstar paid a $110 million settlement to MBIA. In June 2013, Flagstar reached a $105-million settlement with Assured Guaranty. Flagstar paid a $93.5-million settlement to Fannie Mae in November 2011, and $8.9 million to Freddie Mac in December 2013. In September 2014, Flagstar agreed to pay $37.5 million to the Consumer Financial Protection Bureau.

In August 2016, it was announced that Flagstar had repaid all of the funds it received under the Troubled Asset Relief Program (TARP).

The Detroit Pistons of the National Basketball Association announced that Flagstar Bank will be their jersey sponsor for the 2017-18 NBA Season.

Flagstar ranked number 13 on Inside Mortgage Finance's list of Top 50 Mortgage Lenders in 2016. Flagstar Bank services and sub-services loans on a fee basis for others, and services residential mortgages held-for-investment in their own portfolio. In 2016, Flagstar was given the Servicer Total Achievement and Rewards (STAR Award) from Fannie Mae in the General Servicing category.

In September 2016, Flagstar Bank announced its plans for a $10 million economic development program for Pontiac, Michigan. The five-year initiative is aimed at helping revitalize the Oakland County, MI city. The program includes $5 million for home mortgages including a customized home loan product for Pontiac residents, $2.5 million for small businesses and start-ups, $1.5 million for the previously announced naming rights of the Flagstar Strand Theatre for the Performing Arts along with an investment of $1 million for financial literacy in the community.

Thomas J. Hammond, founder of Flagstar, served as chairman of Flagstar Bank and Flagstar Bancorp. Mark Hammond became president of the bank in 1995 and CEO in 2002. In 2009, former CEO of Sovereign Bancorp Joseph P. Campanelli was named chairman, president, and CEO of Flagstar Bank and Flagstar Bancorp. In 2012, Michael J. Tierney, previously executive vice president and managing director of personal financial services at Flagstar, became president and CEO of the organizations. At that time, former vice chairman and director of Comerica Bank and Comerica Incorporated, John D. Lewis was named chairman and director of the organizations. Alessandro P. DiNello became president, CEO and director of the organizations in 2013.

On February 24, 2012, the U.S. Department of Justice ("DOJ") filed a complaint in the United States District Court for the Southern District of New York against Flagstar, alleging that it had been improperly approving thousands of residential home mortgage loans for government insurance. On March 13, 2012 it was announced that shareholder rights firm Robbins Umeda LLP was investigating possible breaches of fiduciary duty and other violations of the law by certain officers and directors at Flagstar Bancorp, Inc.