On her arrival in the UK, 14-year-old Malala will be transferred to Queen Elizabeth Hospital in Birmingham -- an NHS (National Health Service) hospital which has a specialist major trauma centre.
The transfer was kept "top secret" in view of threats to her life, including a warning from the Taliban that it would target her again.
She was accompanied by a team of Pakistan Army doctors and a British medical unit in a specially equipped air ambulance provided by the royal family of the United Arab Emirates.
"The evacuation was arranged by the Pakistani authorities after an assessment by the medical team treating Malala. It follows an offer by the UK government to assist Malala in any way that we could," said a statement issued by the Foreign and Commonwealth Office in London.
"The hospital chosen has the capacity for Malala to be treated without affecting the normal operations of the hospital. Full costs of the medical evacuation, NHS care and any ongoing rehabilitation will be met by the Pakistani government," the statement said.
Talking to reporters in Islamabad, Interior Minister Rehman Malik said the decision to shift Malala to Britain was made jointly by the civil and military leadership.
"We decided to keep the news secret till the flight had taken off from Rawalpindi," Malik said.
The aircraft carrying the teenage girl made a stop in Abu Dhabi to refuel.
"It was agreed by the panel of Pakistani doctors and international experts that Malala will require prolonged care to fully recover from the physical and psychological effects of trauma that she has received," a Pakistani military spokesman said.
"It is expected that in due course of time she will need repair (or) replacement of damaged bones of the skull and long-term rehabilitation including intensive neuro rehabilitation," he said.
Meanwhile, British Foreign Secretary William Hague said his country would stand "shoulder to shoulder with Pakistan in its fight against terrorism".
"The public revulsion and condemnation of this cowardly attack shows that the people of Pakistan will not be beaten by terrorists," Hague said in a statement.
"Last week's barbaric attack on Malala Yousafzai and her school friends shocked Pakistan and the world. Malala's bravery in standing up for the right of all young girls in
Pakistan to an education is an example to us all," he said.
Malala and two schoolmates were shot by the Taliban in her hometown of Mingora in the Swat Valley last Tuesday. She was targeted because she spoke out against the Taliban and campaigned for girls' education.
She was transferred to a leading military hospital in Rawalpindi on Thursday after doctors in Peshawar removed a bullet lodged near her spine.
Earlier in the morning, the air ambulance provided by the royal family of the UAE landed in Rawalpindi and was stationed at the military airbase at Chaklala, located a short distance from the Armed Forces Institute of Cardiology.
Video footage later showed an army medical team transporting Malala on a stretcher.
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