The remains of a man killed at the World Trade Center on 9/11 have been identified nearly 16 years after the terrorist attacks, the city medical examiner said Monday.

The victim’s name was withheld at his family’s request, the ME’s office said. A source told The Post he was not a police officer, firefighter or other first responder.

It was the first new identification of a 9/11 victim since March 2015.

Chief Medical Examiner Dr. Barbara Sampson said the process of testing and retesting remains as DNA analysis becomes more sophisticated helps bring closure to long-suffering families.

“Since the immediate days following the World Trade Center disaster in 2001, the Office of Chief Medical Examiner has worked to identify the victims, and we will continue to uphold this commitment using the most advanced scientific methods available,” she said.

The office uses DNA testing and other means to match bone fragments to the 2,753 people killed by the radical Islamists, who crashed a pair of jetliners into the Twin Towers, igniting an inferno and causing the buildings to collapse.

Remains of 1,641 victims have been identified so far — which means the remains of 40 percent of those who died have yet to be ID’d.

New, more sensitive DNA technology was deployed earlier this year and helped make the latest identification, Julie Bolcer, a spokeswoman for the office, told The Post.

“This is the natural outgrowth of always making improvements and retesting the remains,” she said.

The unidentified remains are stored in a repository at the National September 11 Memorial and Museum, but the testing is done at the ME’s DNA lab in Kips Bay.

Once identified, the victims’ families can decide the remains’ fate.

“Some identified remains are stored at the memorial as well. It depends on what the family wants to do,” Bolcer said.

And as the DNA testing has advanced, so has the multimillion-dollar effort to connect more than 21,900 bits of remains to individual victims. Few full bodies were recovered, and the effects of heat, bacteria and chemicals such as jet fuel made it all the more difficult to analyze the remains.

Over time, the office came to use a process that involves pulverizing the fragments to extract DNA, then comparing it to the office’s collection of genetic material from victims or their relatives.

Additional reporting by Shawn Cohen and Wires