It's the latest honor for Malala, who won this year's Sakharov Prize for human rights from the European Parliament and was nominated for the Nobel Peace Prize.
The 16-year-old told the queen she wants to continue work supporting children's education rights everywhere in the world, including in Britain, where she now lives.
"It's such an honor for me to be here, now in Buckingham Palace, and it was really an honor to meet the queen," Malala told reporters. "Because I also wanted to raise the issue of girls not being educated on a higher platform, so that the government in every country can take action for it. And I have heard that even in the U.K. it's really hard for children to go to school, so we need to fight for education in the suffering countries, in the developing countries, but as well as here."
Malala nearly broke into giggles when the queen's husband, Prince Philip, told her that British parents want their children in school to get them out of the house.
Malala was transferred for medical care a year ago, when she nearly died after being shot in the head in October 2012 while traveling to school in northwest Pakistan.
The Taliban has vowed to try to kill her again.