Hospital said, "the procedures carried out at the hospital were a cranial reconstruction and cochlear implantation."
The spokesperson said "Malala's medical team were very pleased with her progress following the operations which lasted for around five hours on Saturday.
The procedures carried out on her included Titanium cranioplasty which is repairing of the missing area of skull with a titanium plate that has been moulded to accurately replicate the skull.
The other procedure was the Cochlear implant which is fitting a small, complex electronic device that provides a sense of sound to someone who is profoundly deaf or severely hard of hearing.
"Both operations were a success and Malala is now recovering in hospital," the spokesperson said.
Her condition is described as stable and her medical team are very pleased with the progress she has made so far. She is awake and talking to staff and members of her family.
Dr Dave Rosser, Medical Director at Queen Elizabeth Hospital, had earlier said that Malala is unlikely to feel completely normal before 15 to 18 months.
He had stated that there were "lots of ramifications" associated with cranial surgery including "memory loss" and "hormone changes", but that there were no particular concerns for Malala.
Malala was attacked by the Taliban in October after campaigning for girls' rights to education.
A bullet was removed from her head by surgeons in Pakistan, before she was flown to the UK for specialised treatment.
Malala had been discharged as an inpatient from the hospital in January after undergoing weeks of specialist treatment.
The Queen Elizabeth is also home to the Royal Centre for Defence Medicine, which has treated many of the injured servicemen and women returning from Afghanistan.
Earlier this week, Malala was reported to have been nominated for this year's Nobel Peace Prize.
"A prize to Malala would not only be timely and fitting with a line of awards to champions of human rights and democracy, but also ... would set both children and education on the peace and conflict agenda," said the head of the Peace Research Institute of Oslo, Kristian Berg Harpviken.
In December Pakistani President Asif Ali Zardari visited Malala at the hospital.
Malala's family are currently living in the West Midlands.
Her father has been appointed education attache at the Consulate of Pakistan for the next three years.