"I always dreamt of this moment," she told an audience at the office of the prime minister on Wednesday.
Yousafzai, now 20, became emotional during her short speech, pausing to wipe away tears.
"I don’t cry much," she told the crowd, wiping away a few more tears as her family looked on with pride, themselves getting emotional.
Yousafzai established the Malala Fund to help support the efforts of those seeking to educate girls in Pakistan and Afghanistan, two countries where it's long been neglected.
During her four-day trip returning to her country of birth, Yousafzai plans to meet with government officials and female and education activists.
She also had hoped to travel to her native Swat Valley, where she spent her childhood, and to her parents' town of Shangla, where schools have been built through her fund, but those plans were canceled due to administrative reasons, a family source said.
Instead, she'll be privately meeting her family, which will travel to Islamabad. Yousafzai's exact schedule is being closely guarded for security reasons and fear of another attack by the Taliban.
Now a student at Oxford, she said, "I have seen a lot in these years."