Reports said Malala is scheduled to stay in Pakistan until April 2 and will meet with Prime Minister Shahid Khaqan Abbasi on March 29. She also delivered a moving speech about her attack and women's education in Pakistan, CNN reported.
Abbasi praised Yousafzai, saying he is happy to welcome her home, where he says terrorism has been eliminated.
"I have been through tough times from an early age".
"We are fighting a war against terror", he said.
She is frequently attacked by conservative Pakistanis as portraying her country in a bad light and seeking her own fame.
Abbasi praised Yousafzai for her sacrifices and role in the promotion of girls' education.
"It was a month ago when she chose to visit Pakistan at any cost", said a second relative who spoke on the condition of anonymity out of fear of Taliban reprisals.
Marvi Memon, a senior leader of the ruling Pakistan Muslim League party, said called her return a "proud day" for the country.
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.
Yousafzai may visit her childhood home in Swat Valley if security threats don't prevent her from traveling.
"We won't ask men to change the world, we're going to do it ourselves", Malala said.
Tight security greeted the now-20-year-old university student upon her arrival Thursday.
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She miraculously survived the shooting and later went on win a Nobel Peace award for her global campaign for girls' education.
Malala was returning home from school in October 2012 when masked gunmen intercepted her school van and shot her in the head.
"Whether I was in a plane or driving in a vehicle in streets of London, I dreamed of being in Islamabad and Karachi but it was not true".
Her schedule for the four-day trip is being closely guarded.
Opponents were murdered, people were publicly flogged for supposed breaches of sharia law, women were banned from going to market, and girls were stopped from going to school.
Nobel Peace Prize victor Malala Yousafzai says she will continue to campaign for the education of girls in Pakistan.
She has used her Nobel Prize money to build a girls' school in Swat which was inaugurated earlier this month.
"I am just 20-year-old, even then I had endured so much in life, if it were up to me, I would never have left this place", Malala continued to a thunderous applause from the audience.
While her campaigning has taken her around the world, Yousafzai has also harbored a desire to return to her homeland. "She is a source of inspiration for girls in Swat", he said, noting the new school in Shangla in the Swat region.
One leading Pakistani journalist Hamid Mir issued a plea for opposition politicians and commentators not to use bad language when talking about the visit.
Some in Pakistan, especially religious conservatives, have been critical, calling her a polarizing figure who portrays her country in a negative way to seek fame overseas.