"It's kind of a repeat situation of what we went through in October", Lemon said on CNN.
The bomb threat phone into CNN reportedly came from a caller with a Southern accent, MSNBC reports.
The roughly 90-minute drama recalled a similar evacuation in October after an explosive device was discovered at CNN's NY headquarters.
As the 11 p.m. hour began, the network was airing the "Anderson Cooper" episode taped earlier Thursday evening, returning to live programming, about the bomb threat, shortly after 11:15 p.m.
Police closed off 58th Street, where the Time Warner building housing the CNN headquarter is located.
Don Lemon, who was on the air at the time of the bomb threat was forced to abandon his show.More news: Mafia arrests: 84 detained in Europe raids
"All of the employees, all the people who were in the building as we were doing our live broadcast are out of the Time Warner Center now", he added.
Police searched thoroughly the evacuated building and found nothing to substantiate the threat and later gave the all clear.
"The Fake News hates me saying that they are the Enemy of the People only because they know it's TRUE", he tweeted in August.
Journalists at the network confirmed the headquarters had been evacuated while police searched the building.
The network's bureau at the Time Warner Center was evacuated in October after a package containing an explosive device, addressed to former CIA Director John Brennan, was discovered. Sayoc was indicted last month.