Ms Yousafzai, 20, was shot in the head by a gunman for campaigning for female education in 2012.
Her family's home region of Swat was once a militant stronghold, and she was attacked on a school bus there at 15.
It had been unclear if she would visit the area because of security concerns.
On Thursday, it was announced that Ms Yousafzai had returned from the UK to Pakistan for the first time since she was attacked.
Ms Yousafzai delivered an emotional speech at the prime minister's office in Islamabad:
"Always it has been my dream that I should go to Pakistan and there, in peace and without any fear, I can move on streets, I can meet people, I can talk to people.
"And I think that it's my old home again… so it is actually happening, and I am grateful to all of you."
A helicopter carrying Ms Yousafzai landed not far from her family home in Mingora on Saturday, amid a tight security operation.
Her trip to Pakistan is expected to last four days. Officials from her Malala Fund group are travelling with her, local media report.
Why was she attacked?
At the age of 11, Ms Yousafzai began writing an anonymous diary for BBC Urdu about her life under Taliban rule. A documentary film was made about her in 2009.
She soon became a vocal advocate of female education amid militant suppression in Pakistan, and was deliberately attacked on a school bus in October 2012 by Islamist militants. Malala's story brought international attention.
The Pakistani Taliban said at the time that they had shot her because she was "pro-West" and "promoting Western culture in Pashtun areas".
The teenager sustained life-threatening injuries in the attack, and had to have part of her skull removed to relieve swelling on her brain.
After receiving emergency treatment at a military hospital in Pakistan, she was transported to the UK for further treatment and to recover in Birmingham, where her family continue to live.
What has she done since?
Since her recovery, Ms Yousafzai has continued to speak up for children's education and rights around the world.
She set up the Malala Fund with her father Ziauddin, with the goal of "working for a world where every girl can learn and lead without fear".
5 years ago, I was shot in an attempt to stop me from speaking out for girls' education. Today, I attend my first lectures at Oxford.
In 2014 she became the youngest person to win the Nobel Peace Prize. She and Indian activist Kailash Satyarthi were jointly awarded it for their efforts for children's rights.
She has continued campaigning while pursuing her studies, and is now reading Politics, Philosophy and Economics at Oxford University.