Ms. Yousufzai said she always dreamt of returning to the country and living a peaceful life. At the Prime Minister's office, Malala, a 20-year-old now, said it was her dream to come home without any fear.
In 2014, Malala won the Nobel Peace Prize, becoming the youngest victor ever, jointly with India's children's rights activist Kailash Satyarthi for "their struggle against the suppression of children and young people and for the right of all children to education".
Ms Yousafzai was just 14 but already known for her activism when Taliban gunman boarded the school van in which she was sitting and demanded to know "who is Malala?" before shooting her in the head.
Malala began her campaign aged just 11, when she started writing a blog - under a pseudonym - for the BBC's Urdu service in 2009 about life under the Taliban in Swat, where they were banning girls' education. "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 said she remembered having to leave Pakistan for treatment after she was attacked.
Prime Minister Abbasi said he was extremely happy to welcome a daughter of the Pakistan nation who has earned massive fame and respect from the entire world, has come back home. "I want to invest in the education of children.Pakistan women should be empowered". I can't believe that this is happening.
She was awarded Nobel Peace Prize in December 2014.
"That's what we have to fight against, the ideology... that does not accept women as equal to men, that does not accept women to have the right to education, that does not accept women to have the right to do a job, to decide her own future", Yousafzai told Letterman.
The trip is expected to last four days. "Now you are not an ordinary citizen, your security is our responsibility", he said.
It has not been confirmed if she will visit her family's hometown of Swat, once a militant stronghold, in the country's rural north-west during her visit.
Video showed the Nobel laureate clad in a traditional Pakistani shalwar kameez and her head covered in a red and blue scarf as she sat next to the prime minister alongside her parents.
Six women and two girls were among the dead in the incident in Rohri district of Sindh province, 450 kilometres north of Karachi.
Since then, she has become a worldwide symbol of female empowerment, founding the Malala Fund, a charity dedicated to giving all girls access to education, with her father, Ziauddin.
Facebook users also expressed their joy over Malala's return and greeted her with cheerful comments.
The party of Imran Khan, former global cricket star and now leading Pakistani opposition politician, said Yousafzai's return was a sign of the defeat of extremism in the country.