Siyah Bryant, 24, of Jersey City, allegedly climbed a fence onto the airport's tarmac at about 4:20 a.m. Wednesday, the New York Post reported.
He was eventually caught, taken into custody and charged with trespassing.
During questioning, Bryant, who was wearing a pair of women's pants and a sweater, told police that he had been on a date with another man when their car broke down. Bryant's date called another friend, at which point Bryant said he "felt uncomfortable" and left on foot, the report said.
He then scaled the security fence at the airport, walked across two runways and into a terminal, where he was confronted by a United Airlines worker, who called the police, officials said.
The most concerning part of the case is that Newark's new Perimeter Intrusion Detection System, which employs cameras and a sensor-lined fence, did not detect Bryant's presence at the airport, the report said. The system, which is also being used at New York City's JFK and LaGuardia airports and in Teterboro, cost more than $300 million to install.
"The [PIDS] cameras were operating and he was not detected by the PIDS system," an official said.
In August 2012, a person who had been riding a jet ski that ran out of gas managed to get past JFK's PIDS, wander onto the airport's runways and ask workers for help.