The award seeks to recognise Malala's efforts for "the protection of human rights" and especially her fight to protect the right to education without discrimination on "grounds of age, gender, sex and religion," Mexico's official National Council to Prevent Discrimination said in a statement.
The award ceremony is planned for early 2014.
The 16-year-old, who survived a gunshot wound to the head in 2012, has become a global ambassador for the rights of children.
She is currently living in Britain, where she underwent surgery after the attack.
Malala, who since age 11 has written a blog about girls' right to education, has written an autobiography, addressed the United Nations and set up a fund to help girls around the world go to school and promote universal access to education.
Last week, she was awarded the European Union's prestigious Sakharov human rights prize at a ceremony significantly held on World Children's Day.
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