Israeli police spokesman Micky Rosenfeld said around 75,000 prayed at the mosque, the third holiest site in Islam, and that so far there had been no incidents.
Israel's army allows Palestinian men aged over 40 and all Palestinian women in the West Bank to enter Jerusalem without permits until midday on Fridays during Ramadan.
Around 6,000 Palestinians from Bethlehem and Hebron queued at the checkpoint in Bethlehem to enter Jerusalem, said Ayman Ibrahim, head of the traffic police in Bethlehem.
They started arriving at 3 a.m., Ibrahim told Ma'an, adding that the number of worshipers was lower than in previous years.
Palestinian police deployed near the checkpoint from 2 a.m. to maintain security in the area, Ibrahim said.
Palestinian Red Crescent teams were also present from before dawn in case of emergencies, Red Crescent medic Imad Takatka told Ma'an.
An Israeli military liaison official at the crossing told Ma'an that Israeli police had deployed heavily in East Jerusalem.
Um Mohammad, 64, from Hebron, was waiting at the checkpoint and told Ma'an it was her first time to perform Ramadan prayers in Jerusalem.
Alaa Dariyeh, a 24-year-old from Hebron, tried to enter Jerusalem but was turned back from the checkpoint. His application for a permit had been refused, but he arrived at the checkpoint early Friday morning hoping to be allowed to cross.
Rami Barakat, an Israeli military liaison official, told Ma'an that Israeli forces coordinated with Palestinian Authority security services to facilitate the movement of worshipers.
He said the checkpoint had run smoothly and without incident despite the heavy volume of traffic.
JERUSALEM (Ma'an) -- Around 75,000 worshipers prayed at the Al-Aqsa Mosque in Jerusalem for the first Friday of the holy month of Ramadan, Israeli police said.