Sarmed Ozam, 24, told Premier the Home Office had rejected his bid for safety in the UK and instead told him to "go to Baghdad".
Mr Ozam is appealing the decision because he fears he would be killed in Baghdad by Islamic militias: "I can't go back to Iraq, I will be killed there.
"How can I live in a country when the killing of people is Halal and permitted?
"If I did go there I would be a number in the subtitles of the news, the numbers would just be plus one, no one would care about another one on the killed people.
"I would be left dead in the street for the animals."
Mr Ozam was at an Advent reception with Prince Charles hosted by the Archbishop of Westminster, Cardinal Vincent Nichols.
At Archbishop House in central London, the heir to the throne chatted to Iraqi Chaldean Catholic and Syriac Catholic community members.
Mr Ozam explained he thought Prince Charles knowing his personal story was "really important" and said he told the heir his story and what had happened.
He said Islamic State used loud speakers at mosques one night to warn Christians in the city they had to pay a tax, convert to Islam or they would be killed.
When his family left the besieged area the militants took their luggage and left them with nothing.
Speaking about his conversation with Prince Charles, Mr Ozam told Premier: "He said, we will pray for you, we are with you."
A spokesman for Clarence House said he was unable to comment on private conversations the prince had.
Mr Ozam is living in London and is due to find out the verdict of his asylum application appeal in May.
