Fire alarm bells rang out through the building announcing it was being evacuated.
Chief media correspondent Brian Stelter tweeted that CNN was airing taped programming due to the threat.
Don Lemon, who was on the air when the threat forced the abrupt end of his show, also tweeted out the news. The NYPD said they were investigating.
Reacting to the threat, CNN's Chris Cuomo said that everyone was "fine" despite the evacuation.
Just two months ago, bombs were sent to the CNN, as well as top Democrats like Barack Obama and the Clintons.
Police said the building was evacuated and building security did a preliminary search.
Panama Papers fallout: DOJ charges four with fraud The four men were charged in an 11-count indictment Tuesday, and three had been arrested as of Tuesday afternoon. Mr Owens, a 50-year-old Panamanian citizen, worked for Mossack Fonseca as a lawyer and remains at large.
Members of the NYPD's Emergency Services Unit swept the building and gave the all-clear shortly after midnight, reopening it for occupation.
This isn't the first time the building has been the target of bomb threat phone calls.
In October, CNN was targeted in a wave of pipe bombs mailed to the network as well as to prominent critics of President Donald Trump.
The New York Police Department tweeted that they were responding to Columbus Circle, where CNN is located, and urged people to avoid the area.
In October, the building was evacuated after a package with an explosive device addressed to former CIA Director John Brennan was found.