The flag has been hoist above the City Chambers in George Square in a show of solidarity with the French people.
On Wednesday, suspected Islamists killed 12 people at the office of the satirical magazine.
Glasgow made a similar gesture with the Pakistan flag last month after the Peshawar school massacre.
Council leader Gordon Matheson described the killings at the Charlie Hebdo magazine office as "a brutal attack on democracy and freedom of expression".
"Glasgow unites in unequivocal condemnation," he said.
"Our thoughts and prayers are with the victims and their loved ones.
"The murderous actions of perverse and unrepresentative extremists will never overcome a free press which is so fundamental to the values of a democratic society."
He added: "We are flying the flag of France at half-mast from the City Chambers today as a mark of respect for those who have died and to show our solidarity with the people of France and journalists everywhere."
Councillor Matheson and Lord Provost Sadie Docherty plans to write jointly to the mayor of Paris and the French consulate in Edinburgh to express condolences on behalf of the city of Glasgow.
Glasgow City Council is flying the French flag at half-mast as a mark of respect for those who died in the Charlie Hebdo atrocity in Paris.