The comments were made at a Hanukkah reception at the White House on Wednesday as he introduced US evangelical pastor Robert Jeffress to the stage.
Mr Trump said: "Robert Jeffress, I didn't know him, but I watched him, and I'd watch him on different shows. I said,' I like that guy. Man, he talks really great about me', and I like people that talk well about me.
"He was saying, 'He may not be the greatest Christian I've ever seen, he may not know the Bible quite as well as the rest of us, in fact he may not know it very well at all, but that guy's a real leader and he's going to do a job'. I appreciate that statement. I don't know if I should have but I did."
The president's comments were met with laughs from the audience who were there to witness the signing of an executive order to tackle anti-Semitism in US schools and universities.
When Mr Jeffress took the stage for a brief speech he said he believed President Trump "is the most pro-faith president in history".
He also thanked him for being the kind of president, who when it comes to Israel, is on the "on the right side of history, but most importantly... on the right side of God".
He added: "That's why you're not going to fail and we're going stand behind you 100 per cent."
In an interview with Bloomberg Politics in August, Mr Trump seemed to sidestep questions about his knowledge of the Bible.
When asked about what his favourite book in the Bible is, he replied: "I wouldn't want to get into because to me that's very personal ... The Bible means a lot to me, but I don't want to get into specifics."
When the interviewer asked if he had a favourite verse, he said: "No, I don't want to do that."
The journalist persisted and asked the president whether he enjoys the Old Testament or the New Testament.
Mr Trump replied: "Probably equal. I think it's just incredible... the whole Bible. I think it's just incredible. The whole Bible is incredible."
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.