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Sepp Blatter has been FIFA president since 1998.
The announcement comes as a shock as Blatter won reelection last Friday and is just five days into his fifth term as FIFA president, a position he's held since 1998.
FIFA and Blatter have come under heavy fire after the arrest of nine current and former FIFA executives on bribery and corruption charges.
After Blatter was reelected, he told a Swiss TV station that he wouldn't step down because that would mean he did something wrong.
"Why would I step down? That would mean I recognize that I did wrongdoing," he said, via the Telegraph.
Blatter also claimed that he couldn't be held responsible for the corruption in FIFA because it would be "impossible" to preside over everything happening in the organization:
"But how can everybody be responsible? That's impossible ... That is impossible. In no country in the world is there a single court. We are talking about over a billion people. How can a single entity do all that? This needs to be understood. I need to make it be understood ... You can't just ask everybody to behave ethically just like that in the world in which we live."
In the statement announcing his resignation, Blatter said he was stepping down because he lacked the support of the broader soccer world.
"While I have a mandate from the membership of FIFA, I do not feel that I have a mandate from the entire world of football - the fans, the players, the clubs, the people who live, breathe and love football as much as we all do at FIFA," he said.
On Monday, a report in the New York Times by William K. Rashbaum and Matt Apuzzo said that law-enforcement officials believe FIFA secretary general Jerome Valcke, Blatter's No. 2 man, moved money related to an alleged World Cup vote bribe from FIFA bank accounts to an account controlled by arrested FIFA official Jack Warner. FIFA later denied that Valcke was behind the transfer.
FIFA says a new presidential election is likely to take place between December 2015 and March 2016.