The announcement comes after Israeli authorities had shut the mosque compound to worshippers aged under 50 earlier in the day.
The Jerusalem Islamic Waqf, a Jordan-run organization responsible for overseeing the city's Islamic sites, said Israeli authorities had now agreed to lift such restrictions.
"Israeli police will open all gates of Al-Aqsa Mosque without any exception," Firas al-Dibs, a spokesman for the Jerusalem Islamic Waqf, said in a statement.
Al-Dibs later told Anadolu Agency all gates of Al-Aqsa had already been opened, including the Bab Hutta gate.
Eyewitnesses, however, told Anadolu Agency that two gates Al-Asbat and Bab al-Majlis -- one of the main entrances to Al-Aqsa -- had actually been opened.
Earlier, the Palestinian Prisoners' Society said 21 Palestinians from the occupied East Jerusalem had been banned from entering the holy compound for 15 days while the detention of five others had been extended.
Last Friday, Muslims refused to enter the mosque and prayed in the streets surrounding the mosque compound in protest at the installation of metal detectors and other restrictions put in place after two Israeli police officers and three Arab-Israelis were killed.
In southern West Bank, a Palestinian man was shot dead Friday after allegedly trying to stab Israeli soldiers in Gush Etzion, the military said in a statement.
Across the territory, dozens of Palestinians were injured in confrontations with Israeli security forces.
Tear gas caused temporary asphyxia to 23 demonstrators, the Red Crescent added.
Since October of 2015, more than 300 Palestinians have been killed in Israeli-Palestinian violence, according to official Palestinian figures. The Israeli authorities have said at least 55 Israelis have been killed over the same period.