She soon started posting messages on Twitter from the transit area of Bangkok's Suvarnabhumi airport saying she had "escaped Kuwait" and her life would be in danger if forced to return to Saudi Arabia.
"Canada is a country that understands how important it is to stand up for human rights, to stand up for women's rights around the world, and I can confirm that we have accepted the UN's request", he told reporters.
Her case has drawn attention to Saudi Arabia's strict societal rules, including one that obliges women to have the permission of a male guardian to travel.
Canada's decision to grant her asylum could further upset the country's relations with Saudi Arabia.
Before that, Canada and Saudi Arabia were engaged in a diplomatic spat over a federal government tweet criticizing a Saudi civil rights crackdown, prompting the kingdom to expel Canada's ambassador and ordering their citizens studying in Canada to leave.
Their comments included "You're a waste of taxpayer's money", and a BBC official backtracked, with, "We accept that the original wording of our tweet did not reflect the question being posed on air and was open to misinterpretation".
Alqunun had previously said on Twitter that she wished to seek refuge in Australia.
Payne will meet with Deputy Prime Minister and Justice Minister Prajin Juntong as well as holding a bilateral meeting with her Thai counterpart, Foreign Minister Don Pramudwinai, as part of her first official visit to Thailand as foreign minister. "She needs to be protected from those who want to murder her, and should promptly be given asylum in Australia", the commentary said. Bahrain is seeking his extradition. "We will go through those according to our own system and our own process", she said.
The Department of Home Affairs confirmed that the UN High Commissioner for Refugees (UNHCR) had referred 18-year-old Rahaf Mohammed Alqunun to Australia for consideration for refugee settlement.
She refused to fly back and barricaded herself into her airport hotel room, attracting worldwide attention.
Earlier Friday, Australia was assessing a request to resettle Qunun, but hours after tweeting that she had "some good news and some bad news", Thai authorities said she was set to board the flight to Canada.
The fast-moving developments capped an eventful week for Rahaf Mohammed al Qunun.
A Saudi envoy in Bangkok denied any official Saudi involvement in Ms al-Qunun's detention.
Ms Alqunun deleted her Twitter account today, with a friend citing death threats for the decision.
Sophie McNeill, a reporter with the Australian Broadcasting Corporation who has had exclusive access to al-Qunun, said Friday that al-Qunun shut down her Twitter account, but is "safe and fine".
The Associated Press reported last October that Saudi Arabia was paying lobbyists, lawyers and public relations experts almost $6 million (€5.2 million) a year following the disappearance of Saudi journalist Jamal Khashoggiin Istanbul, later admitted as murder.
More recently, Hakeem al-Araibi, 25, a former soccer player from Bahrain who had been granted refugee status in Australia after speaking out against a Bahraini official was detained in late November in Thailand.