Yousafzai and her family met Prime Minister Shahid Khaqan Abbasi in the capital, Islamabad, on her first visit to her homeland since she was airlifted for medical treatment in Britain in 2012.
Clad in a traditional shalwar khameez outfit with her head covered with a red and blue duppata scarf, Yousafzai also met several female Pakistani ministers in the prime minister’s office.
But she is unlikely to travel to her home region of Swat in northwestern Pakistan due to security threats against her, a relative and security sources told Reuters.
“It’s been long-held desire of Malala Yousafzai and her parents to visit Swat and see her relatives and friends. But she was not given permission due to security concerns,” said one relative, who declined to be identified.
Earlier, Pakistan’s Geo TV showed footage of Yousafzai after she arrived at Islamabad airport, walking to a car escorted by security officials.
At the age of 17, Yousafzai became the youngest recipient of the Nobel Peace Prize in 2014 for her education advocacy.
In October 2012, masked gunmen stopped a bus taking Malala and some friends home from school and shot her. Two of her friends were also wounded.
Last week, on Twitter, Yousafzai, who is now 20, expressed a longing for her homeland. She now lives in Britain and is studying at Oxford University.
“On this day, I cherish fond memories of home, of playing cricket on rooftops and singing the national anthem in school. Happy Pakistan Day!” she wrote on March 23.
After surviving the attack, Yousafzai was airlifted abroad and underwent surgery.
The Pakistani Taliban, who seized control of her hometown in Pakistan’s Swat Valley before being pushed out by the army in 2009, claimed the attack in response to her blog for the BBC Urdu service advocating girls’ education.
The hardline Islamist movement blew up girls’ schools and imposed a strict interpretation of sharia Islamic law during their rule over Swat.
The Taliban also accused her of promoting Western values in Swat, which is a staunchly conservative parts of the mainly-Muslim nation.
Unable to return to Pakistan after her recovery, Yousafzai moved to Britain, setting up the Malala Fund and supporting education advocacy groups with a focus on Pakistan, Nigeria, Jordan, Syria and Kenya.
This month, a new girls’ school built with her Nobel prize money opened in Shangla, near her home district of Swat.
During her trip to Pakistan, which is expected to last several days, Yousafzai is expected to stay in Islamabad and meet friends and family at a hotel in the capital, her relatives said.
While she is arguably the most recognisable Pakistani in the world, Yousafzai – known almost universally as Malala – is a polarising figure at home.
She is frequently attacked by religious conservatives as portraying her country in a bad light and seeking fame.
Yet on Twitter her return was greeted broadly positively.
“Welcome back to the home land brave young @Malala,” tweeted Syeda Aqraba Fatima.
“One child, one teacher, one book and one pen can change the world, More Power To You #Malala”