Soccer's world governing body said it brokered the deal that would allow holders of match tickets and a valid Hayya fan ID on flights from Ben Gurion airport in Tel Aviv to Doha's Hamad International during the one-month event.
"With this deal, Israelis and Palestinians will be able to fly together and enjoy football together," FIFA President Gianni Infantino said in the statement.
The statement did not specify which Palestinians, who live in the Israeli-occupied West Bank, East Jerusalem and the Gaza Strip, this might apply to.
The agreement requires Palestinian ticket holders and media "to travel on these chartered flights with no restrictions as they have an equal right to enjoy the tournament," an unnamed spokesperson for Q22, Qatar's tournament operator, said in FIFA's statement.
Israeli Prime Minister Yair Lapid said in a statement that negotiations over several months led to an agreement to open "an Israeli office in Qatar to provide services to fans coming for the World Cup."
Israel's foreign ministry added in a statement that "it was agreed that an Israeli consular team will provide consular services to the Israeli citizens (attending the World Cup).” The statement did not specify where the team would be located.
FIFA said a Doha-based travel company would, in coordination with Israel's foreign ministry, provide consular assistance to Israeli visitors in Qatar during the World Cup, the first to be held in the Middle East and which runs from Nov. 20 to Dec. 18.
In June, when Israel announced that citizens could attend the World Cup in Qatar, Lapid, who is also foreign minister, said it "opens a new door for us to warm ties."
The agreement on direct flights does not change Qatar's stance on normalising relations with Israel which is linked to Palestinian statehood, a Qatari official said.
"This is part of Qatar's commitment to FIFA's hosting requirements and it should not be politicised," the official said. "Because of this agreement, Palestinians will now be able to enjoy the first World Cup in the Arab and Muslim world".
Israeli passport holders can usually only travel to Qatar on special visas issued for sports fixtures or conferences. There are no existing direct flights between the two countries.
A source familiar with the agreement, who declined to be named due to sensitivities, said there were talks with Royal Jordanian Airlines to operate the World Cup charter flights.
The flight arrangement is "subject to Israel's security requirements and operational capabilities" FIFA's statement said.
At least 8,000 Palestinians and 3,900 Israelis have applied for a Hayya card, the source said.
Qatar's Gulf Arab neighbours the United Arab Emirates and Bahrain forged ties with Israel under U.S.-brokered pacts in 2020.
