The landmark presidential contest has become an Asia v Europe battle between Sheikh Salman bin Ebrahim Al Khalifa and Gianni Infantino.
But former FIFA vice-president Prince Ali bin al Hussein is aiming to upset the odds.
And even outsiders Jerome Champagne, an ex-FIFA official, and South African tycoon Tokyo Sexwale, have been doggedly pleading their cause to the more than 200 delegations in Zurich.
The result is uncertain and experts say that football leaders will not be able to escape multi-national corruption investigations even with a new president.
Swiss police, acting under US warrants, arrested seven FIFA officials in Zurich two days before his reelection last May.
Blatter has since been banned from football for six years for ethics breaches and could face criminal charges.
With sponsors holding back on deals and a controversial 2018 World Cup in Russia looming, Sexwale said on the eve of the vote that FIFA was a "broken house".
Infantino, general secretary of Europe's football bloc UEFA, and Sheikh Salman, president of the Asian Football Confederation, have offered starkly different paths for FIFA.
Sheikh Salman, who is seen as closer to the FIFA old guard and has a bedrock of support in Asia and Africa, has said the proposal could bankrupt FIFA.
He said Thursday he would not "mortgage" FIFA's future to win votes.
Each of the rivals has political problems.
Infantino was for seven years the right hand man of Michel Platini, the UEFA president also banned for six years for ethics breaches.
Going into the election, the voting maths is dizzying for Infantino and Sheikh Salman. Both have expressed confidence however.
The AFC and Confederation of African Football (CAF), which between them have 100 votes, have publicly said they are backing 50-year-old Sheikh Salman.
However, Football Federation Australia said Friday it will vote for Prince Ali.
Europe and a big bloc of votes in the Americas are largely behind 45-year-old Infantino.
The election, the prince said "will decide if FIFA goes ahead as we want or if it spirals down."
The congress is also to vote on reforms proposed by a FIFA commission and backed by the body's executive committee aiming to re-establish its credibility.
There will be a 12-year-term limit for the president and other top officials and their salaries will be made public.
Executive committee members will also face greater scrutiny. Many of the 39 individuals now accused by US prosecutors of involvement in more than $200 million of bribes for soccer deals have held high office on the committee.
FIFA's sponsors who are holding out on deals and prosecutors in many countries will be watching the result for signs of football's commitment to reform.
The sport's top leagues want to see a revolution.
"If FIFA and the people in FIFA are not going to act on the message from the whole world that it is time to change...Then the system fails," Jacco Swart, head of the Dutch Eredivisie professional league told AFP.
"We are suffering. Everybody is suffering from this terrible crisis and this terrible image of football," said Frederic Thiriez, head of France's Professional Football League.
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