Yousafzai, who was awarded the Nobel Peace Prize in 2014, has been condemned by some for partnering with Clinton, an outspoken supporter of Israel's war against Hamas.
Khan, who remains behind bars, has been implicated in a range of criminal cases, including charges under the Official Secrets Act, terrorism, and corruption.
Saudi Ambassador to Tehran Abdullah bin Saud Alanazi was present at the airport along with several Iranian officials to send off the first group of pilgrims to Saudi Arabia.