Voting was initially scheduled for Friday but was postponed by a day because of the large number of party members registering as candidates.
Among those seen as leading candidates are Marwan Barghouthi, the party's West Bank secretary-general who is currently being held in an Israeli prison, Jibril Rajub, a former preventive security chief, and Mohammed Dahlan, once Fatah's security chief in the Gaza Strip.
There are strong hopes among the 2,000 delegates that some of the old guard often accused of corruption will make way for younger members of the party, founded by iconic Palestinian leader Yasser Arafat in the late 1950s.
"At the end of the congress, Fatah will have new leadership where the young generation will play a key role," Nabil Shaath, a prominent Fatah member, wrote in the congress's website.
"This will reinvigorate the movement and strengthen its legitimacy."
All Fatah party members will be allowed to vote in person or by proxy, including dozens who were prevented from leaving the Gaza Strip by Hamas, Shaath said.
Tensions with Hamas
Hamas briefly detained a number of senior Fatah members in Gaza on Friday, Fatah said.
Several local Fatah leaders, including Ibrahim Abu al-Naja, Zakaria al-Agha and Abdallah Abu Samhadana were arrested and questioned, an official said. They were released several hours later.
Fatah, which controls the Palestinian Authority, exercised undivided power among Palestinians before it was lost heavily to Hamas in the 2006 parliamentary election.
Longstanding Hamas-Fatah tensions boiled over in June 2007 when Hamas seized full control of Gaza after a week of deadly street clashes, confining Abbas's power base to the Israeli-occupied West Bank.
Corruption allegations have further weakened Fatah over the years.