At 17, Malala is the youngest recipient of the prize.
The announcement was made in Oslo by Thorbjorn Jagland, the committee’s chairman,
The teenager was shot in the head by Taliban gunmen in October 2012 for campaigning for girls’ education.
The BBC reports that the committee said she was awarded the prize “for her heroic struggle against the suppression of children and young people”.
For the previous two years, the prize had been awarded to international bodies: the Organization for the Prohibition of Chemical Weapons in 2013 and the European Union in 2012.
The average age of winners of the prize before Malala is 62.
Pakistan’s Prime Minister Nawaz Sharif congratulated Malala Yousafzai, calling her the “pride” of his country.
“Her achievement is unparalleled and unequalled. Girls and boys of the world should take the lead from her struggle and commitment,” he said in a statement.
Malala was named one of Time magazine’s most influential people in 2013, and awarded the EU’s prestigious Sakharov human rights prize that year.
This year’s record number of 278 Nobel Peace Prize nominees included Pope Francis and Congolese gynaecologist Denis Mukwege, although the full list was kept a secret.
Malala had visited Nigeria few months ago to push for the rescue of over 200 girls abducted by a terrorist group, Boko Haram in April.
During her visit, she met with the Nigerian President, Goodluck Jonathan who told her that the government would do its best to ensure that the girls were rescued.
An Indian child rights activist, Kailash Satyarthi, also won the Nobel Peace prize.
Mr Satyarthi, 60, has maintained the tradition of Mahatma Gandhi and headed various forms of peaceful protests, “focusing on the grave exploitation of children for financial gain,” the committee said at the announcement in Oslo.
Reacting to the news, Mr Satyarthi said: “It’s a great honour for all the Indians, it’s an honour for all those children who have been still living in slavery despite of all the advancement in technology, market and economy.
“And I dedicate this award to all those children in the world”.
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