Malala Yousafzai, in critical condition two days after being attacked in the north-western Swat Valley, arrived by helicopter in Rawalpindi from Peshawar.
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.
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 10m rupee ($105,000; £66,000) reward for information leading to the arrest of the attackers.
Army chief Gen Ashfaq Parvez Kayani, who visited Malala in hospital in Peshawar on Wednesday, said it was time to “stand up to fight the propagators of such barbaric mindset and their sympathisers”.
Malala gained attention aged 11, when she started writing a diary for BBC Urdu about life under the Taliban.
Using 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.
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 Islamabad, Peshawar, Multan and in Malala’s hometown of Mingora and in Lahore.
Those taking part praised the girl’s bravery, while many condemned the attack as un-Islamic.
The attack has also drawn international condemnation.
Former UK Prime Minister Gordon Brown, now the UN special envoy for global education, said Malala Yousafzai had become an “icon for courage and hope” for more than 30 million girls worldwide who are denied primary schooling.
Mr Brown said he had accepted an invitation from President Asif Ali Zardari to lead a delegation to Pakistan in November “to talk about how he can improve opportunities for children”