Malala Yousafzai, in critical condition two days after being attacked in the north-western Swat Valley, left Peshawar by helicopter for Rawalpindi.
The Taliban, who accuse the young activist of “promoting secularism”, have said they will target her again.
There have been widespread protests in Pakistan against the shooting.
Malala Yousafzai was being treated in an intensive care unit in Peshawar before doctors decided to move her to the Armed Forces Institute of Cardiology critical care unit in Rawalpindi.
“Doctors have decided to shift Malala to the Combined Military Hospital [CMH] in Rawalpindi where medical facilities are better,” said Maj Ishtiaq Ahmad.
One of the medical team treating her said “neurologically she has significantly improved” but that the “coming days… are very critical”.
Another doctor, Mumtaz Khan, told AFP news agency that she had a 70% chance of survival.
“Her condition is not yet out of danger despite improvement,” Masood Kausar, the governor of the north-western Khyber Pakhtunkhwa province, was also quoted as saying.
Pakistani officials have offered a 10 million rupee ($105,000) reward for information leading to the arrest of the attackers.
Army chief Gen. Ashfaq Parvez Kayani, who visited Malala Yousafzai in hospital in Peshawar on Wednesday, said it was time to “stand up to fight the propagators of such barbaric mindset and their sympathizers”.
Malala Yousafzai gained attention aged 11, when she started writing a diary for BBC Urdu about life under the Taliban.
Under the pen-name Gul Makai, she wrote about suffering caused by militants who had taken control of the Swat Valley in 2007 and ordered girls’ schools to close.
The Taliban were ousted from Swat in 2009, but her family said they had regularly received death threats.
They believed she would be safe among her own community, but on Tuesday, she was stopped as she returned home from school in Mingora, in north-western Swat, and shot in the head.
Two other girls were injured, one of whom remained in a critical condition on Wednesday.
Schools in the Swat Valley closed on Wednesday in protest at the attack, and schoolchildren in other parts of the country prayed for the girl’s recovery.
Protests were held in Peshawar, Multan and in Malala Yousafzai’s hometown of Mingora and in Lahore.
Those taking part praised the girl’s bravery, while many condemned the attack as un-Islamic.
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