The 16-year-old schoolgirl presented the monarch with a copy of her recently released book, "I Am Malala".
"It is a great honour for me to be here, and I wanted to present you with this book," Malala told her during a reception for Commonwealth, youth and education hosted by the Queen and her husband, the Duke of Edinburgh.
Accepting the gift, the Queen replied: "That's very kind of you."
Malala mentioned how she was sad to have missed a day of school and was passionate about every child having a right to an education, everywhere around the world.
Prince Philip, the 92-year-old known for his quirky sense of humour, joked that in Britain parents sent kids to school to get them out the house, a comment that resulted in a fit of giggles from Malala.
She was accompanied by her father Ziauddin Yousafzai, who also spoke to the royal couple about their past visits to his home country of Pakistan.
Malala has been living and going to school in Birmingham, the city she was airlifted to from Pakistan following the attack by Taliban gunmen last October.
"I was terrified. Where were my parents? Who had brought me there?" she says in her book, in reference to her four operations in Britain and crediting the surgeons for giving her "a second life".
Since the attack she has addressed the UN and been nominated for the Nobel Peace Prize, which she lost out to the chemical weapons inspection team in Syria last week.
But she recently bagged the Sakharov Prize for free speech, awarded by the European Parliament annually in memory of Soviet physicist and dissident Andrei Sakharov.
It included a performance from the Commonwealth Youth Orchestra and Choir.
Meeting high-profile figures and celebrities has become a part of Malala's life as she just returned from a visit to the White House to mark International Day of the Girl last Friday with US President Barack Obama, First Lady Michelle and their daughter Malia.
Undaunted by the occasion, she challenged Obama over US drone strikes in her homeland, saying that they risked "fuelling terrorism".
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