The demonstrators were hurling rocks at an Israeli security force station, located just beyond the compound gate.
Witnesses say the Israeli police dispersed the youth with stun agents. One of the protestors was arrested.
Non-Muslims are prohibited from entering the mosque compound.
Al-Aqsa mosque is considered the third holiest site in Islam after Mecca and Medina in Saudi Arabia.
Muslims believe that Mohammed was transported from Mecca to the mosque currently in Jerusalem's Old City in what they call The Night Journey.
Judaism's Second Temple, destroyed by the Romans in 70CE, was located on the same site at Al-Aqsa.
The disputed area is essentially at the heart of the Palestinian-Israeli conflict.
Today's clash between protestors and police come at a time when escalating tensions between Palestinians and Israelis are drawing a mixed response from the White House and the United Nations.
Analysts believe that whatever happens between Israelis and Palestinians in the next few months may affect the UN General Assembly vote this September on the membership of a Palestinian state, which would drastically affect the future of the long-time adversaries' relations.