Incumbent President Sepp Blatter is seeking a fifth term. His only challenger is Prince Ali bin al-Hussein of Jordan.
The vote of FIFA’s 209 members comes two days after seven top officials were held in Zurich in a US fraud inquiry that indicted 14 people.
Sepp Blatter, 79, has faced calls to quit but says he is not responsible for the scandal and is favorite to win.
Both Sepp Blatter and Prince Ali bin- al-Hussein, 39, will have 15 minutes to address the delegates.
Each of the 209 member associations can then vote.
In the first round, a candidate must get two-thirds of the votes to win outright, or 140 votes.
If that is not achieved there will be a second round requiring a simple majority, even though there are only two candidates.
Sepp Blatter, who is in office for 17 years, remains the favorite, with strong support in Asia, the Americas and Africa.
At the congress opening on May 28, Sepp Blatter addressed the issue of corruption, insisting it fell to him to “fix things”.
He said: “We cannot allow the reputation of football and FIFA to be dragged through the mud and it has to stop here and now.”
However, Sepp Blatter distanced himself from the scandal, saying: “Many people hold me ultimately responsible for the… global football community… I cannot monitor everyone all of the time. If people want to do wrong they will also try to hide it.”
He said the “actions of individuals” had brought “shame and humiliation on football”.
Prince Ali bin al-Hussein has the support of most of Europe.
Responding to the scandal, Prince Ali said that FIFA needed leadership that “accepts responsibility for its actions and does not pass blame… and restores confidence in the hundreds of millions of football fans around the world”.
He said: “I am a straightforward person with straightforward ideas and ethics – a person who loves our sport.”
The head of European football’s governing body, UEFA, Michel Platini, was one of those calling for Sepp Blatter to quit.
At an emergency meeting with other FIFA confederation heads and Sepp Blatter on May 28, Michel Platini said he had asked the president “as a friend” to resign, saying: “I have had enough – enough is enough, too much is too much.”
Sepp Blatter refused, and the other confederations agreed with him that Friday’s vote should go ahead.
Two criminal investigations were announced on May 27.
The US investigation accuses those indicted of bribery, racketeering and money-laundering involving tens of millions of dollars over 24 years since 1991.
It includes allegations of bribes to influence the outcome of bids to stage football tournaments such as the 2010 World Cup in South Africa and the 2016 Copa America in the US.
Two FIFA vice presidents were among those arrested in Zurich.
One of them, Jeffrey Webb, was on May 28 “provisionally dismissed” as head of the Confederation of North, Central American and Caribbean Association Football (CONCACAF).
Swiss prosecutors have launched a separate investigation into the bidding process for the World Cup tournaments in 2018 in Russia and 2022 in Qatar.
Meanwhile, many of FIFA’s major sponsors have expressed concern over the investigations.
Coca-Cola, Visa, Adidas, McDonald’s, Hyundai Motor and Budweiser are pressing FIFA to take immediate action to restore its reputation.
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