They have been "horribly treated," he said.
In an interview with the Christian Broadcasting Network Trump said: "Do you know if you were a Christian in Syria it was impossible, at least very tough to get into the United States?
"If you were a Muslim you could come in, but if you were a Christian, it was almost impossible and the reason that was so unfair, everybody was persecuted in all fairness, but they were chopping off the heads of everybody but more so the Christians.
"I thought it was very, very unfair. So we are going to help them."
On Friday Trump signed an executive order suspending all refugees arriving from Syria and six other countries for four months so that "extreme vetting" measures can be put in place.
It is unclear how this policy will match up with his commitment to help Christians.
"We want to ensure that we are not admitting into our country the very threats our soldiers are fighting overseas," Mr Trump said as he signed the order at the Pentagon.
"We only want to admit those into our country who will support our country and love deeply our people."
Elsewhere in his interview with CBN Trump said he had "always felt the need to pray" and that being president meant he needed God "even more".
"There's almost not a decision that you make when you're sitting in this position that isn't a really life-altering position. So God comes in even more so," he said.
