"We demand the resignation of the Fatah central committee, the revolutionary council and local [party] leaders," the demonstrators shouted through loudspeakers as they broke down the compound gate.
Saturday was the second consecutive day of protests in which thousands of Fatah supporters demanded the party leadership's resignation after the party's crushing electoral defeat to Islamist group Hamas.
Protesters broke down the gates of the Gaza branch of the Palestinian Legislative Council, which had been reinforced after a similar incursion on Friday, but security forces inside offered no resistance.
The crowd held aloft pictures of Yasser Arafat, the late Palestinian leader and Fatah founding father, as well as yellow flags of the party, while gunmen fired into the air.
"We did not come to show our power to the media but to call for the resignation of the Fatah central committee and to give a chance [at power] to our young leaders," they shouted.
Men and women carried automatic weapons and rocket-propelled grenade launchers in a good-tempered demonstration as poetry and songs about Fatah blared from the sound system, along with speeches by the late Arafat.
"We did not come to show our power to the media but to call for the resignation of the Fatah central committee and to give a chance [at power] to our young leaders"
The crowd then moved on to the house of Mahmoud Abbas, the Palestinian president, where a few adolescents tried to get into the heavily secured compound, insulting Abbas. Their comrades pulled them down from the wall and called for calm.
"We will stay on your path, Abu Ammar [Arafat]," they shouted before moving on to Gaza City's Centre for Preventative Security.
"Preventative security will stay with Fatah."
The loudspeakers announced another Fatah demonstration at a sports stadium in Gaza City the following day.
The protest came just hours after Muhammad Dahlan, a re-elected Fatah MP, told AFP that a planned Fatah protest in the city had been postponed in an attempt to preserve the peace.
Thousands of protesters clamoured outside the parliament building in Gaza City late on Friday, setting fire to three parliament cars and demanding that Fatah should not take part in any new government led by Hamas.
Meanwhile, the final results of the Palestinian legislative election gave Hamas 74 parliamentary seats, while President Abbas's Fatah faction won 45, a source close to the parties told journalists on Sunday.
Senior Hamas officials are
preparing a new government
The Palestinian source said the official announcement for the 132-member parliament - the second such ballot held since 1996 - would be announced later in the day.
Earlier unofficial results gave Hamas 76 seats against 43 for Fatah.