Fatima Sheikh, a 16-year-old from Dhaka, will take on the role of the teenage activist who was shot by the Taliban last year and was airlifted to the UK for life-saving surgery.
The further details Sheikh's identity are being kept under wraps until the shoot begins in the middle of July.
"She is a student too. She looks like Malala. But there are security issues. Filming will take place in London, Pakistan, Iran and India," British newspaper 'The Independent' quoted the Kolkata-based director as saying.
Malala, who also appeared in a subsequent documentary about her work as campaigner, was shot in the neck after her school bus was intercepted by a Taliban gunman last October.
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They said they had intentionally targeted her because of her work and her alleged links to the West.
Malala's shooting triggered outrage across Pakistan and around the world and she was later nominated for the Nobel Peace Prize.
Khan said he had been inspired by her struggle for the right of girls in Pakistan's Swat Valley.
Malala has since resumed her schooling at Edgbaston High School for Girls in Birmingham and is currently visiting the UAE to perform the Umrah pilgrimage.
"This is a private visit to the Kingdom dedicated toward performing Umrah. Malala is keen on performing several Umrahs during her visit and wishes to spend time alone in the Haram Al-Sharif. She is authoring a book and attending school. She has to prepare for her exams and therefore was not able to meet more people," Malala's father, Ziauddin Yousafzai, told 'Arab News'.