Blatter announced his decision at a press conference in Zurich on Tuesday, four days after being re-elected for a fifth term and six days after the arrests of 14 Fifa officials ahead of Friday’s congress.
The 79-year-old confirmed he will hold position until a successor is elected.
“I have thoroughly considered and thought about my presidency and the last 40 years of my life,” Blatter said.
“These years were closely related to Fifa and the wonderful sport of football. I appreciate and love Fifa more than anything else. I only want to do the best for Fifa and my institution.
“I felt compelled to stand for re-election, as I believed that this was the best thing for the organisation. That election is over but Fifa’s challenges are not. Fifa needs profound restructuring.
“My mandate does not appear to be supported by 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.
“The interests of Fifa are very dear to me and that is why I have taken this decision (to resign). An extraordinary congress is to be called to elect my successor as soon as possible.
“Since I shall not be a candidate, I am therefore now free from the constraints that elections inevitably impose.”
A minimum four-month notice period is required for Fifa to hold congress, while candidates will also need to be vetted.
An election time frame of between December 2015 and March 2016 has been given by Domencico Scala, the independent chairman of the organisation’s Audit and Compliance Committee.