"In the outside world, internationally, there are concerns that Pakistan is a terrorist country or there is no peace in Pakistan", she said.
It's still the "most handsome place on earth", the young Nobel Laureate says.
The visit was kept highly secret and hardly anyone knew until she landed in Islamabad and was driven in security to a hotel.
After flying from Islamabad, she met with friends and family before visiting the all-boys Swat Cadet College Guli Bagh, a military-run school some 15 kilometers outside Mingora.
On the afternoon of 9 October 2012, Yousafzai was injured after a Taliban gunman attempted to murder her. Yousafzai remained unconscious, in critical condition at the Rawalpindi Institute of Cardiology, but later her condition improved enough for her to be sent to the Queen Elizabeth Hospital in Birmingham, UK.
Most Pakistanis warmly welcomed her visit but some launched a campaign on social media against her and she also faced tough questions from journalists.
Yousafzai's fund has already built a school in Swat and she says schools are needed to fight extremists.
Footage on local television channels showed the 20-year-old and her family arrive at Benazir Bhutto International Airport in capital Islamabad to board a plane to the United Kingdom after a four-day visit.
In an exclusive interview with Ayaz Gul for the Voice of America, Yousafzai said it was important for her to come back to Pakistan.
Her near-miraculous recovery, and tireless career as an education advocate, have since turned her into a global symbol for human rights, and in 2014 she became the youngest person ever to be awarded the Nobel Peace Prize when she was just 17.
Malala told AFP in Swat that she could see vast changes in the area since 2012-but added she has read reports which claim up to 50 percent of children are still out of school.
Following the Taliban shooting, Malala left Pakistan for the United Kingdom, where she has lived ever since.
The Taliban, who are opposed to the education of girls, have destroyed hundreds of schools in Pakistan.