Khatib was barred from the complex after inciting violence in media interviews and in sermons at mosques.
He is considered the most prominent figure in the movement since its leader, Sheikh Raed Salah, was jailed until the end of legal proceedings against him as he too faces incitement charges.
"I am returning to the al-Aqsa Mosque after three years in which I was prevented from coming to the mosque and to Jerusalem," he said in a video filmed at the complex. "This decision prevented the 'landlord' from entering to his home. The Israeli occupier is preventing us from entering the al-Aqsa mosque."
Khatib continued with a threat, "I want to tell Israel: Your decision to ban the Islamic Movement is unjust. You thought you could keep the people from the al-Aqsa Mosque, but you saw what happened last July when you tried to put metal detectors and cameras at the gates of the mosque."
Israel added security measures at the Temple Mount after three Israeli Arab terrorists from Umm al-Fahm opened fire at a police patrol from the complex, killing two Israeli police officers, Ha'il Satawi and Kamil Shnaan. The additional security measures led to rioting in east Jerusalem and across the country.
Before being barred from al-Aqsa, Khatib made similar warnings, saying, "The continuous harm done to the al-Aqsa Mosque and opening it to Jews has led to great anger. If talk of dividing the mosque area continues, the situation would explode not just in Jerusalem but in the entire region and the whole world. The Palestinian people will not remain silent. (Prime ministers) Rabin and Sharon are gone, but the al-Aqsa Mosque remains. (Prime Minister) Netanyahu will also go, and the mosque will remain."
Maor Tzemach, founder of the movement "For You, Jerusalem," condemned the decision to allow Khatib to return to the Temple Mount. "This decision constitutes the crossing of a red line in the fight against incitement. Khatib is among the leaders of the northern branch of the Islamic Movement, incites against the State of Israel on a regular basis and organized a support rally for Sheikh Raed Salah in Umm al-Fahm," he said.