The vote comes on the eve of Yousafzai's visit to Canada where she'll participate in an event on women's rights in Toronto.
The teen is being made an honorary Canadian in recognition of her bravery in her fight for the rights of women and girls to go to school, Prime Minister Stephen Harper told the House of Commons on Tuesday.
Yousafzai, now 17, became the target of Taliban assassins for being an outspoken advocate for the right of girls to go to school in her region of Pakistan.
She survived an attempt on her life two years ago and has since gone on to become an international spokesperson for the importance of access to education.
"She serves as a model and an inspiration to Canadians and to the entire world in her fight for universal education," Harper said in the motion.
The Conservatives announced their intention to make her Canada's sixth honorary citizen in last year's throne speech.
Nothing more was said until earlier this month when Yousafzai was declared as the co-winner of the Nobel Peace Prize and the government announced she was coming to Canada.
She is scheduled to attend an event called "Strong Girls, Strong World", being hosted by the government at a Toronto school Wednesday afternoon.
The prime minister's office said the event "will focus on empowering young girls through meaningful discussion, to continue being leaders and voices of change in their communities."
She'll then officially be given her citizenship in a ceremony with Harper and Citizenship and Immigration Minister Chris Alexander at a downtown hotel.
Harper and Yousafzai have met before: the two sat down together on the margins of a United Nations event in New York City last year.
There's no official procedure involved in making someone an honorary citizen though precedent has been for the House of Commons and Senate to approve a motion before the honour is officially granted.
"We are honouring Malala today but really it is our honour for us to bring her within the family of Canadian citizens because her aspirations mirror the very best of our own values," Liberal Senator James Cowan said during the Senate debate on the motion.
"Today we are standing as a nation and telling the world: 'we are all Malala.'"
Five other people have been made honorary Canadian citizens in the last 30 years: Raoul Wallenberg, Nelson Mandela, Aga Khan, Aung San Suu Kyi and the 14th Dalai Lama.
According to the Citizenship and Immigration Department, honorary citizenship is just a symbolic title and individuals do not, for example, get passports or the right to vote.
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