The council had offered Suu Kyi the Freedom of Glasgow in 2009 when she was still under house arrest as Myanmar’s pro-democracy leader.
"I and the Leader, Councillor Susan Aitken, recently wrote to Aung San Suu Kyi voicing the city's concerns about the human rights atrocities occurring under her watch and urging her to intervene. The response we received was disappointing and saddening,” said Glasgow's Lord Provost Eva Bolander.
The Scottish council said that withdrawing such an honour was "unprecedented" and its decision had not been taken lightly.
Glasgow's decision follows a similar decision by the city of Sheffield, which stripped Suu Kyi of the Freedom of Sheffield earlier this week, saying she had shown "willful ignorance" of the crisis.
"In response to the ongoing humanitarian crisis in Myanmar of the Rohingya people, various UK cities have revoked the Freedom of the City from Aung San Suu Kyi. I'm delighted there was cross-party support for my motion," said Councillor Soryia Siddique from Sheffield Council.
Meanwhile, the London School of Economics (LSE) has taken the first step towards withdrawing an honorary presidency bestowed upon Myanmar’s de-facto leader.
The Students Union has moved a motion to withdraw the honour, which will come up for debate next week.
A spokesperson for the LSE Students Union said: "Suu Kyi's choice to prioritise her tenure in office over anything else has come at too significant a cost, her complicity in the ethnic cleansing of the Rohingya people.
"We condemn the Muslim genocide in Myanmar, we condemn all Islamophobia, and we will actively work against any system which is complicit in supporting the violence."
A series of UK institutions have been distancing themselves from the Nobel Peace laureate in the wake of Myanmar Army’s repression of the Rohingya minority, nearly 1 million of whom have fled their homes to refugee camps in Bangladesh.