In a letter to Fouad Massoum the Pontiff urges him to try and put an end to the "brutal suffering" of Christians.
Militant group I.S. (formerly ISIS) has been advancing across large parts of Iraq forcing religious minorities to leave their homes.
In one area the extremists gave an ultimatum to Christians to convert to Islam, pay a tax or face death.
The Pope's envoy to Iraq, Cardinal Fernando Filoni, delivered the letter which said: "I appeal to you with my heart full of pain while I follow the brutal suffering of Christians and other religious minorities who are forced to leave their homes, as their places of worship are destroyed."
Yesterday the Holy Father phoned the family of murdered journalist James Foley to offer his condolences.
He was killed by I.S. fighters who later released footage of his death.
Elsewhere At least 68 people have been killed in a mosque in eastern Iraq.
Shia militants are understood to have opened fire on Sunni Muslims there.
Meanwhile the UK government's ruled out forming any alliance with the Syrian regime to fight extremists.
Some people believe Bashar Al-Assad could help defeat the militants and former British Army chief of staff Lord Dannatt thinks it we may have to work with him: "For Islamic State to be properly faced down it's going to have to be engaged in Syria.
"There are two or three options, one of which is that some form of engagement has to be reached with Assad government.
"That's pretty unattractive."
Foreign Secretary Philip Hammond says such a move wouldn't be 'practical, sensible or helpful'.
The call comes as the UN's top human rights official accused the world of forgetting about Syria.
Navi Pillay's comments come as the death toll from the country's civil war has risen to more than 191,000.
Nadim Nassar is a Syrian Anglican priest based in London. He told Premier's News Hour a string of globally significant events has pushed the cival war there down the news agenda: "After Syria we had Iraq, Ukraine, Russia and all the international aspects of that."
He added that he thinks the UN death toll is very conservative: "I think we're far beyond even 250,00 to 300,000 dead in Syria."
Hear more from Nadim Nassar here: