While Abbas's advisers insist the congress is being held because it is overdue, some analysts see it as an opportunity for him to sideline allies of his exiled longtime rival Mohammed Dahlan.
Talk of who will eventually succeed Abbas as Palestinian president has intensified, with the ageing leader not having publicly designated a successor.
A recent hospitalisation for a heart test has only added to such talk, but Abbas has maintained that he has no intention of stepping down anytime soon.
The congress to last up to five days in the occupied West Bank city of Ramallah is expected to be key for the future of the secular party and the Palestinian Authority it controls.
It is to include elections for Fatah's central committee -- in which Abbas serves as president -- and its revolutionary council, considered Fatah's parliament and which has more than 120 members.
The 1,400 Fatah officials invited to attend the congress are to vote for 18 members of the central committee and 80 seats on the revolutionary council, while the rest are to be nominated.
Observers see the reduced number of officials to vote -- down from more than 2,000 in 2009 -- as part of a move to exclude Dahlan supporters.
Now in exile in the United Arab Emirates, Dahlan was expelled from Fatah in 2011 and has faced a series of legal cases since.
Abbas's term as Palestinian president officially ended in 2009 but there has been no election since due to an ongoing dispute between his party and its main rival, Islamist movement Hamas.
The Palestinian parliament has not met since 2007.
Fatah -- which controls the West Bank -- and Hamas have been at loggerheads since the latter seized the Gaza Strip in a near civil war in 2007.
Dahlan fell from grace in June 2007 after the humiliating rout of his forces by Hamas in week-long street battles that saw the Islamists expel Fatah from the coastal enclave.
The Gaza-born politician was expelled from Fatah in 2011 over allegations of financial corruption and murder.
The Palestinian high court in 2015 upheld a presidential decree lifting Dahlan's parliamentary immunity, sparking condemnation from civil society activists.
That "cannot be taken out of context: one of political infighting within Fatah around the person of lawmaker Dahlan," political analyst Jihad Harb said of the lifting of his immunity.
Fatah has become increasingly intolerant of dissent from the party line, Harb said.
The party is the main component of the Palestine Liberation Organisation and led the movement to sign the 1993 Oslo Accords that gave birth to the Palestinian Authority.
Hamas and the Islamic Jihad -- the two most powerful forces in Gaza -- have never joined the PLO.
Recent opinion polls have suggested most Palestinians would like Abbas to step down.
Political analyst Abdel Majid Abu Sweilam says that, beyond staving off Abbas's rivals, the congress also aims to reinforce Fatah's hold within the institutions of the Palestinian Authority.
The congress will also address the Israeli-Palestinian peace process, stalled since early 2014.
It will be Fatah's seventh congress since its founding in 1959 and the first since 2009.
The 2009 meeting saw younger officials enter the central committee including Marwan Barghouti, currently imprisoned, as well as Jibril Rajoub and Dahlan.
Polls have shown that Barghouti would win if an election for Palestinian president were held today, but he is jailed for life for murder by Israel over his role in the second Palestinian intifada.
Rajoub, a former head of intelligence, now leads the Palestinian Football Association and has been an advocate for the Palestinian cause within the sport.