A Korean Air flight carrying Ms Alqunun left Bangkok for Seoul on Friday night at 11:37pm Bangkok time, a Thai airport official said. No other details were immediately offered.
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.
Marise Payne met with senior Thai officials in Bangkok a day after Australia announced it would assess the request for asylum by 18-year-old Rahaf Mohammed Alqunun, who was stopped Saturday at a Bangkok airport on her way to Australia and her passport seized.
Qunun was granted UNHCR refugee status after she locked herself inside a hotel room at the Bangkok International Airport and launched an international social media campaign to prevent Thai authorities from deporting or handing her over to her family.
Under Saudi Arabia's "male guardianship system", a Saudi woman is required to obtain a male relative's approval to apply for a passport, travel outside the country, study overseas on a government scholarship, get married, leave prison, or even exit a shelter for abuse victims.
Several Saudi women fleeing abuse by their families have tried to seek asylum overseas in recent years but have been sent back home.
The case is the latest in a series highlighting what human rights activists say is the widespread subservient treatment of women in Saudi Arabia.
Rahaf Mohammed al-Qunun walking with an unidentified companion in Bangkok, Thailand.
Canada's apparent decision to accept Qunun could further upset its relationship with Saudi Arabia.
A Saudi teenager who fled her homeland for Thailand to escape her "abusive" family is to fly to Canada, Thai officials say.
Around midday on Friday, Qunun posted on her Twitter account that she had "bad and good news!"
Qunun, who is staying in Bangkok at an undisclosed location and was not available for comment, had earlier said on Twitter she had been receiving death threats from a relative on the social media platform.
Separately, she told AFP she had suffered physical and psychological abuse from her family, including being locked in her room for six months for cutting her hair.
On Friday, Trudeau avoided answering a question about what the case would mean for relations with the kingdom, but he said Canada will always unequivocally stand up for human rights and women's rights around the world.
Although her asylum case has moved at lightning speed the final maneuvers that led to her flight to Canada remain a mystery.
Australia said on Wednesday that it was considering taking in Qunun.
Australia's Foreign Minister Marise Payne met with senior Thai officials in Bangkok, where Ms al-Qunun is now located, on Thursday. Among those arrested was Samar Badawi, whose family members fled to Canada in 2015 and have since become Canadian citizens.
Payne is also expected to discuss the case of a Bahraini footballer with Australian asylum status who has been jailed in Thailand and faces extradition back to Bahrain.
In a statement to 10 daily, a spokesperson for the department said it would consider her referral for resettlement in Australia.