The undisclosed gift from the Prince of Wales's Charitable Foundation was made to Catholic charity Aid to the Church in Need (ACN), and came after His Royal Highness made a speech about persecuted Christians at an advent reception hosted by Cardinal Vincent Nichols, the Archbishop of Westminster, last month.
During his address the Prince of Wales warned that the crisis in the Middle East and the growth of extremism could threaten "the very existence of Christianity in the land of its birth".
The Prince met with Iraqi and Syrian Christians with direct experience of persecution and heard about their experiences.
Neville Kyrke-Smith, National Director of Aid to the Church in Need in the UK, thanked the Prince for his solidarity with the persecuted Church in the Middle East: "Having met Iraqi and Syrian refugees recently in Lebanon, I know how much such help means - and the fact that our brothers and sisters are not forgotten.
"The support of The Prince of Wales for the work of Aid to the Church in Need and other organisations encourages more people to do the same."
In December the charity announced a series of extra emergency aid for people in the Middle East, including 30 new projects in some of the worst affected areas.
Facilities like showers, washbasins and toilets were built for displaced Christians in Erbil in Kurdish northern Iraq, as well as a nursery school for 125 toddlers.
