No details about the passenger were immediately released, and the bus remained parked in downtown Portsmouth with a bomb squad on the scene.
"He is in custody," police Capt. Mike Schwartz said. "No one is injured."
The ordeal began around 11:30 a.m. Thursday when a passenger called 911 to report an explosive device on board, leading police to evacuate buildings and streets and call the passengers out under the watch of a sharpshooter in an armored vehicle. One man remained on board and did not walk out until just before 9 p.m.
The man, wearing camouflage pants without a shirt, stepped off the bus with his hands high over his head. He then went to his knees before soon getting up and appearing to follow orders from police to walk away from the bus.
Throughout the day, police kept the curious at a distance and gave little information of what was happening on the bus. They said they established a way to communicate with the remaining passenger but wouldn't give details of that communication.
Passenger Danielle Everett, 20, of Poland, Maine, said she didn't see anything suspicious on the bus.
"It really wasn't any big deal," said Everett, who was met at the Portsmouth police station by her concerned father.
Family members of some other passengers who gathered at the police station said their relatives did not feel threatened aboard the bus; several said the passengers were confused and more frightened by the police response.
The 911 call came after the bus arrived in the seaside city of Portsmouth and was "based on someone's observations," Schwartz said. He had not heard of any threat being made.
The driver "received a report of suspicious activity" while making the routine stop on the trip from Bangor to New York City and followed his training to secure the bus and notify police, Greyhound spokeswoman Maureen Richmond said.
The driver parked the bus and got out, but the passengers remained on board for more than two hours while police surrounded it and cleared the area of people. When they did leave, it was very slowly, separated by several minutes each. They carried no purses or bags, and most held their hands aloft as they passed officers with their weapons drawn.
Passengers were screened individually when they got off the bus - much like an airport security check - and were taken to the police station to be interviewed. None appeared to be injured as they left the bus; Schwartz said one was taken to a hospital because of a medical condition.
Some passengers resumed their trip on a replacement bus just before 8 p.m., an hour after the original bus had been scheduled to arrive in New York. Others skipped the trip and were picked up. Greyhound said it would arrange to reunite passengers with their luggage and personal items they were forced to leave behind.
Joe Law, of Hudson, N.H., said he was walking toward his parked car when he saw the bus pull over. Law said the driver got off, ran to the back of the bus and pulled part of its back door down. He said the driver appeared to do something to disable the bus, then yelled, "get away from the bus," before running down the street.
During the standoff, the state police explosives disposal unit and the FBI were on the scene, and restrictions were put on air travel in the area, which kept television helicopters from flying overhead at closer than 3,000 feet.
The bus was parked with its flashers on, between a municipal parking garage and the Hilton Garden Inn. The hotel, garage and other area businesses had been evacuated, and streets were closed.
Associated Press reporters David Sharp in Portland, Maine, and Holly Ramer in Concord, N.H., contributed to this report.