Malala, 17, was shot in the head in 2012 by the Taliban near her home in Swat Valley for her advocacy of girls' right to go to school.
"Millions of children have voted to award Malala this year's World's Children's Prize for the rights of the child," the organisation said in a statement.
"Nobody has ever received the Nobel Peace Prize and the World's Children's Prize - often dubbed the 'Children's Nobel Prize' by the media - in the same year."
The award was created in 2000 and is part of a worldwide educational programme in which children learn about global issues, democracy and their own rights.
The programme finishes with a global vote on who to give the prize to.
This year's honorary awards went to former Microsoft executive John Wood, founder of the Room to Read literacy group, and Indira Ranamagar from Nepal, for her work for the children of prisoners.
Nelson Mandela, Graca Machel, Anne Frank and Kofi Annan have previously been honoured in the awards.
Malala will receive the prize at a ceremony in Mariestad near Stockholm on Wednesday.
This year's laureates will share $100,000 to be used in their work for children's rights.
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With a plethora of awards given to her, the day is not far when the main distinction of any award will be "this is the rare award which Malala didn't win"
If I hear one more 'award' of this 'sweet' girl then I am sure to get diabetes . I have had just about 'enough' .
Congrats!!! but would you like to share what have you actually done besides taking a bullet?
You deserve every prize, every medal, every award, ever accolade you get......and don't let anyone tell you otherwise.