The Zionist police also reportedly detained two guards as they surrounded the compound, entering through the Chain Gate.
Scores of worshipers were inside the mosque as it was surrounded.
Dozens of people were removed, harassed and assaulted, the International Middle East Media Center reports.
Meanwhile, all men below the age of 50 were prevented from entering the mosque grounds.
The Al-Aqsa mosque is considered to be the third holiest place of worship for Muslims.
According to the latest social media reports, the raid is still ongoing.