Israel bombed the radar station and control tower on 4 December 2001 and bulldozers cut the runway on 10 January 2002, rendering the airport inoperable.

It was designed by Moroccan architects (modeled after Casablanca airport) and engineers funded by Morocco's King Hassan II.

By mid-2000, a handful of foreign carriers, including Royal Air Maroc and Egyptair, had introduced flights to Gaza as well.

[9] Israel alternated between reopening and shutting down the airport over the next several months before finally prohibiting all commercial air traffic on 13 February 2001; from then on, only Arafat's private aircraft were allowed to use the airfield.

[12] On 15 November 2005, after the end of the intifada and the Israeli unilateral withdrawal from the Gaza Strip, Israel and the Palestinian Authority (PA) signed the Agreement on Movement and Access that provided: "The parties agreed on the importance of the [Yasser Arafat International] airport.

Since March 2006, no discussions have taken place between Israel and the Hamas government in the Gaza Strip, including in relation to the airport.