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.
She met with the prime minister in Islamabad and later gave an emotional speech at his residence.
Earlier, tight security greeted the now-20-year-old university student upon her arrival at Pakistan's Benazir Bhutto International Airport.
Some say that Yousafzai return signifies the end of extremism in Pakistan and hopefully in the world at large.
"So it's actually heartening, and I am grateful to all of you", she added.
"God willing, Pakistan, the future of Pakistan, lies in its people", she said. Local media speculated she might visit the school.
Many on Twitter called for a warm welcome for the activist after news of her overnight homecoming broke.
Malala's shooting had caused outrage across the globe.
Shahid Khaqan Abbasi said she was just a child when she left, but has returned as the most prominent citizen in the country.
Security in the country has greatly improved in recent years, with the number of attacks carried out by militants drastically reduced. "I know that millions of girls around the world are out of school and may never get the opportunity to complete their education", Malala wrote at the time. She expressed her love for Pakistan and insisted that the South Asian country not be considered as extremist.
"Welcome home", Prime Minister Abbasi told Yousafzai. Social media was flooded with people's reaction: some appreciating her bravery while others says that her visit will foment dissent. "Your enemies were those monsters who shot her point blank on her way to school". Malala's story brought worldwide attention.
Eleven people were killed and nine injured when the roof of a warehouse collapsed onto workers in southern Pakistan on Wednesday, officials said. The bullet grazed her brain and lodged in her neck.
What has she done since?
"I have noted that the girls in Swat and elsewhere in Pakistan see Malala as their own and believe that whatever she is doing is meant for them", he said. She was later awarded the 2014 Nobel Peace Prize for her work in championing education for young women and girls across the world.
Instead of being silenced by the 2012 attack that gravely wounded her, Yousufzai went on to become a globally recognized advocate for moderation and children's education.
Yousafzai is now pursuing her Bachelor's Degree in Politics, Philosophy and Economics at Oxford University's Lady Margaret Hall, while continuing to further her movement for women's rights. "I would have never left the country had the doctors not advised to get treatment in the United Kingdom", she said.
"There is this lust for change".
Yousafzai's return Thursday made instant news in Pakistan.
Ali stressed that the organisation went on a countrywide strike in order to show solidarity with Malala when she was attacked.
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