In a statement, the agency said Derek Fenton was fired on Sept. 13 because his public actions "violated New Jersey Transit's code of ethics" and "violated his trust as a state employee."
NJ Transit spokeswoman Penny Bassett Hackett said Fenton, 39, had worked for the agency for 11 years as a train conductor and most recently as a coordinator to ensure the right number of train cars is put into service.
Republican Gov. Chris Christie agreed with the transit agency's decision.
"We are supportive of the action taken by NJ Transit," Christie spokesman Michael Drewniak said.
A phone message left Wednesday morning for Fenton at his home in northern New Jersey was not immediately returned, and the number was disconnected by Wednesday afternoon. No one answered the door bell at Fenton's home Wednesday night even though lights were on and people appeared to be inside and two cars were in the driveway.
It could not be determined if Fenton had retained a lawyer.
The NJ Transit action raised questions about whether Fenton's First Amendment right to free speech was violated, a legal expert said.
"A person can't be fired for off-the-job political expression when that person is employed in a non policy-related role," said Ed Barocas, legal director for the New Jersey chapter of the American Civil Liberties Union.
NJ Transit's code of ethics states that employees must give notice to an ethics liaison officer before participating in political activities. Once that is done, it says, an employee can participate in political activities so long as state or federal law or agency rules don't explicitly prohibit them and so long as "the activity doesn't conflict with the employee's official duties."
It's unknown whether Fenton submitted the paperwork.
The Koran desecration occurred on the ninth anniversary of Sept. 11, 2001, the day Islamic extremists flew planes into the World Trade Center and killed nearly 2,800 people. Police grabbed Fenton during the desecration and escorted him away but did not arrest him.
Muslims consider the Koran to be sacred, and any intentional damage or show of disrespect to the Koran is deeply offensive.
The leader of a small Christian congregation in Gainesville, Fla., had planned to burn copies of the Islamic holy book to mark the Sept. 11 anniversary but called off his plan at the last minute. Pastor Terry Jones' plan had drawn opposition across the political spectrum and around the world. President Barack Obama had appealed to him on television, and Gen. David Petraeus, head of the U.S. mission in Afghanistan, said carrying out the plan would have endangered American troops.
On Wednesday, state Sen. Ray Lesniak called Fenton a "self-centered, irresponsible person who would put American lives in jeopardy without thinking," but he said Fenton's actions are constitutionally protected.
"We need to keep our heads while others are losing theirs," said Lesniak, D-Union. "Mr. Fenton needs a good talking to by community and religious leaders, not a one-way ticket to unemployment."
Fenton burned the pages near the lower Manhattan site where a Muslim group wants to build a 13-story Islamic center and mosque, just blocks north of ground zero. Opponents of the planned mosque location argue it's insensitive to families and memories of Sept. 11 victims to build there, while proponents support the project as a reflection of religious freedom and diversity.
A Facebook page titled Help Derek Fenton has been set up to help Fenton find a new job.