The release a day after a judge granted her bail is another step closer to ending an episode that has focused an uncomfortable spotlight on Pakistan's harsh blasphemy laws, which can result in life in prison or even death for defendants. Many critics say the laws are misused to wage vendettas or target Pakistan's vulnerable minorities like the Christians.
The jail official, Mushtaq Awan, said the girl left the prison in Rawalpindi, a garrison city near Islamabad amid tight security.
An Associated Press reporter on the scene said she was taken from the prison in an armoured vehicle and whisked to a waiting helicopter while covered with a sheet to protect her identity.
A Muslim cleric from her neighbourhood was arrested last week for planting evidence to incriminate the girl, an about-face in a case that has drawn strong international condemnation. Even in Pakistan where there is significant support for punishing people accused of desecrating the Quran or insulting Islam's Prophet Muhammed, the girl's age and questions about her mental state have earned her a degree of public sympathy often lacking in other blasphemy cases.
Her lawyers say they will now push to have the case against her thrown out entirely.
"Her parents were with her when she was freed from the jail, and she has been taken to a safer place," said a member of her legal team, Tahir Naveed Chaudhry.
The girl's release came a day after a judge in Islamabad granted bail to the mentally challenged girl, a move hailed by the human right activists and representatives of Pakistan's minority Christian community. Bail is rarely granted in blasphemy cases, and the decision signals a degree of sympathy that could result in all the charges being dropped.
The girl, who medical officials say is 14 years old, was arrested Aug. 16, shortly after hundreds of angry Muslims surrounded her house, and accused her of burning pages from the Quran, an act punishable by life in prison. Her lawyer has denied the allegation.
But in a sudden turn-around, police arrested a cleric after a follower from his mosque accused him of stashing pages of a Quran in the girl's bag to make it seem as if she burned them. He allegedly planted the evidence to push Christians out of the neighbourhood and is now being investigated for blasphemy himself. He has denied the allegation.
The arrest was applauded as a rare occurrence when blasphemy accusers are held responsible for false claims.
In his ruling granting bail, the judge wrote that the arrest of the cleric cast serious doubt on the prosecution's case. He also said she was a minor, had mental challenges and that it was "not believable" that she had intentionally burnt the Quranic verses. On those grounds, he decided to grant the bail.
The tight security present during her release is a sign that authorities are taking her safety seriously in light of previous attacks on people accused of blasphemy. Two prominent politicians were gunned down last year for suggesting the blasphemy laws should be amended to prevent misuse. The killer of one of the politicians was later lauded by supporters who threw rose petals whenever he appeared at court.
A man in the central Pakistani city of Bahawalpur was beaten to death in July by an angry mob after he was accused of blasphemy.