Malala was shot in the head in 2012 by the Taliban near her home in Pakistan for supporting the rights of young girls to attend school.
Millions of children voted for the 17-year-old to win her latest prize, said the World's Children's Prize organizers 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," it added.
Malala was in Mariefred, south of Stockholm, to collect the award on Wednesday afternoon. The prizes were handed out in the Gripsholm Castle in a lengthy ceremony attended by Queen Silvia and Prime Minister Stefan Löfven.
Prime Minister Stefan Löfven meets with Malala. Photo: TT
Press and curious onlookers flocked to the castle for the awards. Photo: The Local
Queen Silvia presented the awards in Sweden after a ceremony on Wednesday, which included musical performances from children around the world. Malala was scheduled to have a private audience with new Prime Minister Stefan Löfven afterwards.
The World's Children's Prize was created in 2000 as part a worldwide educational programme designed to help 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, other 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 with the children of prisoners.
Nelson Mandela, Graca Machel, Anne Frank and Kofi Annan have previously been honoured.
This year's winners will share a prize of $100,000 to be used in their work for children's rights.