One of which was to Esther, a Nigerian who was abducted as a teenager by Boko Haram militants.
Jeremy Hunt's letter to her stated: "I cannot begin to imagine the horrors of what you have suffered. I stand in awe of the great faith that has given you the strength to rebuild your life and dignity.
"I want you to know that you are not alone that British diplomats continue to raise your situation that we continue to fight your corner and that we stand with those who are being denied the basic rights to practice their faiths."
Erin James from religious freedom charity Open Doors told Premier she was shocked to discover Mr Hunt had written the letters.
"I've certainly not heard about it before," she said.
"So we are at Open Doors absolutely thrilled to see him engaging with Christians like this."
She said Esther reacted similarly to the letter when the charity delivered it.
"Esther was completely shocked when this letter came through," she explained.
"She couldn't believe that he even knew who she was. So it's so wonderful - at Open Doors we're about family and we're about supporting our persecuted family.
"So it's so wonderful to see that girl realise how supported she is, how loved she is by Christians in the UK and around the world."
The charity's founder Brother Andrew also received a letter from Mr Hunt praising Open Doors.
The letters come as the Foreign and Commonwealth Office announced recently a review into the persecution of Christians.
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