The Pakistan army provided Malala a helicopter, which took her to Mingora, her hometown, from Islamabad, where she arrived on Thursday with her father and younger brother, the Guardian reported.
The social activist arrived in Islamabad on Thursday on her first Pakistan tour since she was shot by a Taliban gunman as she was returning from her school in Swat valley on 9 October 2012.
It was Yousafzai's first visit to her homeland since she was shot in late 2012 and airlifted overseas for medical treatment.
The visit - on which she was accompanied by her father, mother, and two brothers - was kept tightly under wraps. I've never been so happy before.
Two security officials told Reuters that the trip by helicopter would likely be just for one day.
"God willing, we will counter the terrorism and extremism in our region with the weapon of education, with the weapon of a pen, with the weapons of teachers and with the weapons of books".
In a letter, written by Adnan Rashid, the Taliban militant, claiming the attack on Malala Yousafzai in 2012, it was highlighted that the attack on Malala was because of her belief that "pen is mightier than the gun".
Unable to return to Pakistan after her recovery, Malala moved to Britain, setting up the Malala Fund and supporting local education advocacy groups with a focus on Pakistan, Nigeria, Jordan, Syria and Kenya.
Last year, she was accepted for a Bachelors degree programme at Oxford University in the United Kingdom, where she has resided since receiving treatment there in 2012 for wounds sustained in the attack.
Malala returned to Pakistan on a four-day visit late Wednesday night.
The youngest Nobel laureate said she would return to Pakistan after completing her education.
The Taliban had later issued a statement saying that if Malala had survived the attack, then she would be targeted again.
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.
"Tears of joy rolled down Malala's eyes during her meeting with them".
That was the year she was attacked by the Taliban for advocating girls' education.
"What I want is for people to support my objective of education and think about the daughters of Pakistan who need an education", she told the newspaper. I don't want any favour or I don't want everyone to accept me.
At the age of 11 she began sending diary entries to BBC Urdu that told what it was like living under the Taliban. "My treatment here [Pakistan] was by Army doctors and if they had not done my surgery in time I would not be here today".
Residents say Malala's story has changed the lives of other girls in the area. She remained there, enrolling at Oxford University in August 2017 and has resumed her fight for the cause that earned her the Nobel Peace Prize in 2014.
The school is now providing quality education to at least 183 students, majority of them being in the ages between 5 and 12, while at least 38 of them are orphans.
"Her courage is an example for education in a place called Swat".