Medical staff said she was well enough to be discharged as an in-patient following the surgery last weekend, Sky News reported.
The hospital said the 15-year-old will now continue her rehabilitation at her family's temporary home in Birmingham and will visit occasionally for outpatient appointments.
It said her family had asked for the media to respect their privacy and dignity at this time.
Malala was shot in Pakistan's conservative Swat Valley on October 9 and was air-lifted to the Queen Elizabeth Hospital on October 15 for further specialist treatment. She received bullet wounds just above her left eye.
Malala had earlier this month undergone two successful operations to attach a titanium plate and cochlear implant.
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.