The "Malala Schools" are planned for 16 areas around Pakistan affected by conflict or natural disasters, Nafisa Shah, chairwoman of the National Commission for Human Development, said.
The aim is to give children in these areas, who often have little in the way of educational opportunities, a chance to go to school, Ms Shah said, but added that money for the scheme had not yet been found.
"We have identified the places and (will) soon launch a fundraising scheme to generate finances for these schools," Ms Shah said.
Each school will have two classrooms, a verandah, a toilet and space to extend the building if needed. It will cost Rs 800,000 ($8,220) and provide basic education to both girls and boys.
The Pakistani government has announced a plan to pay poor families to send their children to school and UN education envoy Gordon Brown held talks in Islamabad at the weekend to begin a plan to bring more than five million out-of-school youngsters into the classroom.
Taliban hitmen shot Malala on her school bus a month ago in Mingora in Pakistan's northwestern Swat Valley in a cold-blooded murder attempt for the "crime" of campaigning for girls' rights to go to school.
Miraculously the 15-year-old survived and her courage has won the hearts of millions around the world, prompting the United Nations to declare last Saturday a "global day of action" for her.