Israeli police attacked Palestinian worshippers with rubber bullets, tear gas and stun grenades after Friday prayers in Jerusalem's Old City , injuring 55 people, local media reported.
Of the 55 wounded, 20 were shot with rubber bullets and 30 suffered asphyxiation from the tear gas, the director of the Arab Health Center told Ma'an news agency.
Police arrested 15 people after storming Al-Aqsa, a spokesperson said.
"The police stormed the compound and dispersed the stone-throwers using stun grenades," spokeswoman Luba Samri told AFP. "One policeman was injured and 15 of the protesters were arrested."
Jews, who also pray at the compound, celebrated the second day of their new year, or Rosh Hashana, on Friday, and police had stepped up their presence in and around the Old City for the occasion.
It houses the Al-Aqsa and Dome of the Rock mosques  and is the third holiest site in Islam after Mecca and Medina in Saudi Arabia.
Jews worship at the bottom of the Western Wall, venerated as the last remnant of wall supporting the Second Temple complex, which was destroyed by the Romans in 70 AD and considered Judaism's holiest site.