The event has been hosted annually in Washington DC since 1953.
In his address, Trump thanked the people who had said they were praying for him throughout his campaign.
He added: "America will continue to thrive as long as we have faith in each other and faith in God.
"Freedom of religion is a sacred right, but it's also a right under threat all around us and the world is under serious, serious threat in so many different ways."
Trump appeared to have been referring to the executive order temporary blocking people from seven countries, including Syria, from entering the country. The move has been heavily criticised by a number of Christian leaders.
He added: "I've never seen it so much and so openly. We're going to straighten it out. That's what I do, I fix things. It's time we're going to be a little bit tough."
"We must never stop asking God for the wisdom to serve the public according to his will," Trump concluded.
Yesterday, Trump tweeted a photo of members of his administration praying together after Evangelical Judge Neil Gorsuch was nominated for the US Supreme Court.
Moment of prayer last night after my nomination of Judge Neil Gorsuch for #SCOTUS. It was an honor having Maureen and Fr. Scalia join us. pic.twitter.com/caYOwmeMuG— President Trump (@POTUS) February 1, 2017
Trump also vowed to repeal the Johnson Amendment, an IRS rule which bars ministers from endorsing candidates from the pulpit.
He said: "I will get rid of and totally destroy the Johnson Amendment and allow our representatives of faith to speak freely and without fear of retribution."
An overwhelming number of Evangelicals voted the US president into office ahead of Hillary Clinton.