Birmingham's Queen Elizabeth Hospital said a titanium plate and cochlear implant were successfully attached in two operations yesterday.
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.
A hospital spokesperson said she was continuing to recover and was in a stable condition after the surgery, which lasted five hours.
They said the medical team was "very pleased" with the progress Malala had made so far and that she was awake and talking to staff and members of her family.
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.
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.
