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 is expected to hold meetings with Prime Minister Shahid Khaqan Abbasi.
Details of the trip have been kept secret "in view of the sensitivity", an official told AFP news agency.
Pakistani television broadcast video that appeared to show her with her parents at Islamabad's Benazir Bhutto International Airport under tight security.
The trip is expected to last four days and she arrived with officials from her Malala Fund group, local media report.
It has not been confirmed if she will visit her family's hometown of Swat in the country's rural north-west during her visit.
Many on Twitter called for a warm welcome for the activist after news of her overnight homecoming broke.
What a pleasantly surprising news ! @Malala expected in Pakistan tonight ! Welcome to your motherland, daughter of the soil, pride of the nation ! Give her the utmost love, everyone !
Return of #Malala is another evidence of extremists defeat Inshallah… Lets not be divided by suspicions lets give @Malala respect and honor she deserves … Welcome #MalalaInPakistan
Pakistan’s daughter and the global symbol of female education is back in Pakistan. Welcome home @Malala.
Why was she attacked?
At just 11, Ms Yousafzai began writing an anonymous diary for BBC Urdu about her life under Taliban rule.
A vocal advocate of female education amid militant suppression in Pakistan, she was deliberately attacked on a school bus at 15. Malala's story brought international attention.
The Pakistani Taliban said at the time that they 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 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 last year earned a place at Oxford University.
Is Pakistan still dangerous?
Despite security efforts in recent years, the Pakistani Taliban has remained active.
They have been blamed for a number of deadly attacks on schools and colleges that have killed hundreds.
Ms Yousafzai repeatedly expressed her wishes to return to Pakistan, describing her hometown of Swat as "paradise on earth" in an interview earlier this month.
"I have received a lot of support in my country," she told US talk-show host David Letterman in a Netflix special.
"There is this lust for change. People want to see change in their country. I am already doing work there but I want my feet to touch that land."
Pakistan is religiously conservative and late last year Ms Yousafzai was trolled online after a picture of her in Oxford wearing western clothes – jeans and heeled boots – was shared on social media.