The "Day of Rage" is set to take place on Wednesday over new security measures introduced at the weekend by the Israelis after police were attacked at the site, known to Muslims as the Noble Sanctuary and to Jews as the Temple Mount.
The al-Aqsa Mosque compound is a flashpoint Islamic site, which is also holy to Jews.
Israeli police said last night that some 200 Palestinians tried to block a road nearby and threw stones at officers who dispersed them.
The news comes after the controversial Israeli closure of the mosque, deemed the third holiest site in Sunni Islam, to Muslims and tourists on Friday, following an attack on Israeli police the same day.More news: South Korea offers dialogue with the North to ease border tensions
In addition, Netanyahu reiterated his pledge via the White House that Israel would maintain the status quo at the site, the report noted, adding Jordan was also involved in the communications.
Jews are allowed to visit but not pray there to avoid provoking tensions.
The new security arrangements, which include metal detectors, are Israel's response to the deadly attack that claimed the lives of two Israeli Druze police officers, Kamil Shnaan and Haiel Sitawe.
The site remained closed on Saturday, while parts of Jerusalem's Old City were also under lockdown.
The attack triggered a rare phone conversation between Netanyahu and Palestinian President Mahmoud Abbas, who condemned the attack and called for the site to be reopened.More news: State police release drawing of suspect in Delphi killings
Fatah Central Committee Member Jamal Muhaisen said that protest is necessary until the metal detectors are removed. 'I assume that with time they will understand that this is not bad, ' he told Army Radio.
A Palestinian driver rammed his vehicle into a group of Israeli soldiers in the occupied West Bank on Tuesday and was shot dead by the troops, the Israeli military said.
During that period, Israeli forces have killed more than 254 Palestinians, a lot of them said by Israel to be attackers while others were killed in clashes with Israeli forces.
Muslims have been refusing to enter because of the metal detectors, with Palestinians viewing the move as Israel asserting further control over the site. Israeli officials said they were a permanent measure but many worshippers refused to go through them and preferred to pray outside the compound.More news: Donald Trump's Climate Change Denial Ignites the Grass Roots