The award was received Tuesday on behalf of Malala by Shiza Shahid, the coordinator of Malala Fund for Girls' Education, at the UN General Assembly's commemorative meeting to mark the 65th anniversary of the Universal Declaration of Human Rights, the Associated Press of Pakistan (APP) reported.
South Africa's late anti-apartheid icon Nelson Mandela and former US president Jimmy Carter are among the eminent recipients of the prize, which is conferred every five years.
Malala was conferred the award for speaking out on girls' right to education, women's empowerment and the links between the two.
"Malala's courage, commitment and determination, and more so, her passion for human rights at a tender age makes us proud of her," APP quoted Pakistan's delegate to the event Diyar Khan as saying, while thanking the UN for recognising her contribution to promoting girls education and honouring her courage and sacrifice.
"We're grateful to the international community for the support to the Malala Fund for Girls' Education, and hope it would advance the cause of literacy in my country and around the world," he said.
Malala could not attend the event due to commitments in her school in Birmingham, England, where she now resides.
Other winners of the prize in Tuesday's event were Biram Dah Abeid of Mauritania, a son of freed slaves who works to eradicate the scourge of slavery; Hiljmnijeta Apuk of Kosovo, a campaigner for the rights of people with disproportional restricted growth; Liisa Kauppinen of Finland, the president emeritus of the World Federation of the Deaf; and Khadija Ryadi, former president of the Morocco Association for Human Rights.
Mexico's Supreme Court of Justice also received a prize as a judicial body, the APP report said.