The billboards are emblazoned with the strapline: "To all of our atheist friends: Thank God you're wrong."
The digital billboard in Times Square measures 45 feet by 90 feet and is an unmissable bright blue.
In addition to the cordial message, passers-by are encouraged to visit the website of Answers in Genesis (AiG), the sponsors of the advertisements, where they can read articles and watch a video that present the case for God's existence.
Ken Ham, president of AiG and the Creation Museum stated: "In a friendly way, we want to reach out to people in secularized parts of the country and share the hope we have in Christ.
"Atheists live in a world of ultimate meaninglessness and purposelessness. But the good news is that God sent His Son to offer the free gift of salvation. There is purpose and meaning in life. And we thank God for that."
Three billboards with the same message have also been placed in San Francisco, including one at the east entrance to the Bay Bridge.
In the Los Angeles area, billboards will be placed this month on Sunset Boulevard and another on the busy Santa Ana Freeway, one of the busiest freeways in America.
"More than ever, people are asking us to prove that there is a God," Ham continued. "I tell them our faith is not a blind faith but a reasonable one.
"Furthermore, Romans 1:20 says that the creation of the world by God is so clearly seen that none of us has any excuse for rejecting God.
"At the same time, AiG understands that atheists like Richard Dawkins look at the same evidence and interpret it differently in light of their humanistic worldview. But theirs is not a reasonable faith."