Malala met the Queen and the Duke of Edinburgh at Buckingham Palace during a reception for people who work in education.
The Queen described the campaigning work of the Pakistani teenager, who survived an assassination attempt by the Taliban, as "wonderful".
She listened intently and nodded as Malala spoke of her aim for every child to have an education, and added: "It's wonderful, isn't it?"
Malala had a fit of giggles as the Duke then told her: "There's a thing about children going to school - they go to school because the parents don't want them in the house."
The teenager gave the Queen a copy of her book, I Am Malala, which the monarch accepted, adding: "That's very kind of you. Thank you very much indeed."
After meeting the Queen, Malala said that she would not ordinarily miss a day of lessons - but made an exception on this occasion.