Ms Yousafzai, now aged 20 and a vocal human rights activist, was shot in the head by a gunman for campaigning for female education in 2012.
In an emotional speech at the prime minister’s office, she said it had been her dream to return “without any fear”.
Pakistani television broadcast video showing her arriving with her parents at Islamabad’s Benazir Bhutto International Airport under tight security.
“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,” Ms Yousafzai said in a televised address from the PM’s house in Islamabad.
“And I think that it’s my old home again… so it is actually happening, and I am grateful to all of you.”
The trip is expected to last four days. Officials from her Malala Fund group travelled with her.