Michael Fawcett, chief executive of the foundation, had initially agreed to suspend his duties following newspaper revelations about his links to a Saudi national.
Dr. Shakil Afridi helped the CIA track down al Qaeda chief Osama bin Laden in 2011.
Qureshi had been on the run since 20 blasts ripped through Gujarat's main city Ahmedabad on July 26, 2008, killing more than 50 people.
Shakil Afridi: The doctor who aided hunt for Osama bin Laden languishes in Pakistan prison, forgotten
Many might wonder how Pakistan could imprison a man who helped track down the mastermind of the 9/11 attacks.
A top American Senator has announced that he will introduce a bill that would eliminate US aid to Pakistan and set the money aside for infrastructure funds to build roads in the US.
Al-Qaeda's slain chief Osama bin Laden had shifted to Afghanistan to supervise a plot to assassinate Pakistan's former premier Benazir Bhutto and then military dictator Pervez Musharraf.