The flag was raised at the City Chambers on George Square yesterday despite opposition from some politicians and some in the Jewish community.
Glasgow is the second local authority in Scotland to fly the flag after West Dunbartonshire did so last week. Fife Council plans to follow suit.
Nearly 1900 Palestinians and 67 Israelis have been killed since fighting between Israel and Hamas began in early July.
The Disasters Emergency Committee said the violence has left the entire population of Gaza without adequate access to medical care and about 1.4 million people have no water and sanitation, or very limited access to it.
Hundreds of thousands of people have fled their homes and 65,000 homes haved been ruined.
Glasgow Lord Provost Sadie Docherty wrote to Bethlehem mayor Vera Baboun on Wednesday, stating the city's support.
She said: "In solidarity with Bethlehem and Palestine, Glasgow City Council will raise the Palestinian flag on Friday August 8. We hope that peace can be found to ensure the human rights for the people of Palestine."
A spokeswoman for Glasgow City Council said last night that there were no plans to fly the flag again, though it was not ruled out.
Fife Council plans to fly a Palestinian flag at its Glenrothes headquarters for a week. Council leader David Ross said there was a "general consensus" in favour of the gesture to raise awareness of the suffering of people in Gaza.
"This action is not in support of any specific organisation but simply in solidarity with the people of Gaza," he said.
Tory councillor David Meikle flew an Israeli flag from his office window in Glasgow's City Chambers yesterday. He said Glasgow's decision to fly the Palestinian flag was made without consulting councillors. It would do nothing to stop suffering on both sides of the conflict and could cause division in the city, he added.
A statement from the Israeli embassy in London said: "Whilst the Palestinian flag flies over Glasgow, the flag over Gaza is the green Hamas flag, which expresses the one-sided ideology of blind hatred, which the group shares with Al-Qaeda, Boko-Haram, Isis and other radical Islamist entities."
Paul Morron, president of the Glasgow Jewish Representative Council, said: "I think this is gesture politics. I think it will not alleviate the suffering of one person in the Middle East conflict and I don't think it will bring peace closer." Mr Morron said the move instead has the potential to cause division.
But there was support for Glasgow from the group Scottish Jews for a Just Peace. Marion Hersh from the group said: "We are particularly distressed by the Israeli bombardment of Gaza, leading to the deaths of nearly two thousand Palestinians. We support Glasgow City Council in flying the Palestinian flag and consider it a welcome gesture of solidarity and support."
A small number of protesters gathered outside the City Chambers for a peaceful demonstration.
l Scottish aid charity SCIAF has made an emergency appeal to help people in Gaza. SCIAF is helping to get food, water, medicine and blankets to those in urgent need. To donate visit www.sciaf.org.uk or call 0141 354 5555.