There was a heavy police presence as Khalid Chishti was lead into court
Imam Khalid Chishti allegedly told a witness that this was a "way of getting rid of Christians", a prosecutor said.
The girl, named as Rimsha, is said to be about 14 and to have learning difficulties.
The case has sparked international condemnation.
Earlier this week, a court extended Rimsha's detention at a maximum-security prison by a further two weeks.
Her father has said he fears for his daughter's life and for the safety of his family. He has called on Pakistani President Asif Ali Zardari to pardon her.
Rimsha's parents have been taken into protective custody following threats, and many other Christian families have fled the neighbourhood.
Pakistan's strict blasphemy laws are often used to settle personal vendettas, correspondents say.
Last year two leading politicians were assassinated after speaking out against the legislation.
'Proven conspiracy' Imam Chishti appeared in the Islamabad court with a white blindfold and shackled hands.
There was a large police presence as he was ushered into the building.
"The imam was arrested after his deputy Maulvi Zubair and two others told a magistrate he added pages from the Koran to the burnt pages brought to him by a witness," an investigator Munir Hussain Jaffri said.
He said Mr Zubair and some others had told the imam not to interfere, urging him to "give the evidence to the police as he got it".
According to Mr Jaffri, Imam Chishti had told them: "You know this is the only way to expel the Christians from this area."
The investigator said the cleric had been arrested at his home on Saturday under Pakistan's blasphemy law.
"By putting these pages in the ashes he also committed desecration of the Holy Koran and he is being charged with blasphemy," he said.
The girl's lawyer told AFP news agency that Rimsha "should be acquitted immediately", as it had been "fully proven that it was a conspiracy".
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