The hospital said President Zardari, accompanied by his daughter Asifa Bhutto, met doctors who have been treating Malala since her admission to the hospital on 15 October.
"They were brought up to date on the 15-year-old's medical progress and her future treatment plan by (the trust's) medical director, Dr Dave Rosser," the statement added.
President Zardari and Asifa Bhutto then had a short five-minute private meeting with Malala, her father Ziauddin and her brothers Khushal Khan and Atal Khan.
The President appreciated the courage and conviction of Malala and described her as a "remarkable girl" and a "credit to Pakistan".
He also thanked the hospital staff for their outstanding care.
Malala was shot in the head by the Taliban in the Swat Valley of north-west Pakistan on October 9 when she was returning from school with two classmates.
The Taliban had said that she was targeted for espousing secularism and Western ideals.
Doctors said the bullet grazed the teenager's brain when it struck just above her left eye. She was flown to Birmingham to receive treatment unavailable in her own country.
Tens of thousands of people have since then signed a petition, seeking a Nobel Peace Prize for Malala.