The Nobel laureate, whose arrival in the country dominated headlines and social media, broke down in tears as she delivered an emotional televised speech Thursday saying it was a "dream" to be home.
But with intense criticism among the many messages of welcome, her itinerary was being kept under wraps over security fears, with even those meeting her not being told of her presence until the last moment.
Malala Yousafzai, left, and her parents pose for a photograph with the Prime Minister of Pakistan in Islamabad. Source: AAP
Malala is widely respected internationally as a global icon for girls' education, but opinion is divided in Pakistan, where some conservatives view her as a Western agent on a mission to shame her country.
"Pakistan has not done well by its heroes," an editorial in English-language Dawn newspaper on Malala's homecoming said Friday, noting that the country's other Nobel laureate - physicist Abdus Salaam - had been widely shunned for being a member of the persecuted Ahmadi minority.
Women's rights activist Nighat Dad said that she and a group of other feminists from across Pakistan who were gathered on Thursday were not told they would be meeting Malala until the last moment.
The organiser, Oscar-winning director Sharmeen Obaid-Chinoy, only told them "It'll be the highlight of your year," Dad said - adding that she had been right.
Malala Yousafzai's book, 'I Am Malala', is her story of survival after she was attacked by the Taliban. Source: AAP
Malala's schedule for Friday was not clear, though there was some speculation she would return to her native Swat, where she was shot and where, earlier this month, a school built with her Nobel prize money was opened.
Malala became a global symbol for human rights after a gunman boarded her school van on October 9, 2012, asked "Who is Malala?" and shot her.
The Pakistani Taliban accused her of "anti-Islamic" activities and of "smearing" the militant group in statements released after the attack.
She was treated for her injuries in the British city of Birmingham, where she also completed her schooling.
The youngest-ever winner of the Nobel Peace Prize in 2014, she has continued to be a vocal advocate for girls' education while studying at Oxford University.
Swat, in Pakistan's rugged northwest, was overrun by the Taliban in 2007, where they imposed a brutal regime including banning girls from school.
They were pushed out in a military operation in 2009, but security has remained fragile, as the attack on Malalathree years later demonstrated.
However in recent weeks authorities have lifted prohibitions against tourists visiting the mountainous region, famed for its beauty, as security improves.
