A sign outside the train flashed "All Aboard" in red letters.
The conductor gave a broad all-clear wave, stepped inside and the train glided out of the station at 5:30 a.m.
Passenger Raphael Kelly of New York, looking relaxed, said he was "feeling fine" and had "no worries."
Kelly, who takes Amtrak to Philadelphia weekly, said with a smile that if he did have any concerns, "I have to get over it."
Kelly said that if anything, the train might be safer than ever.
Read MoreAmtrak budget cut looms amid historic US budget surplus
"They're on their toes" because of the crash, he said.
At a service Sunday evening at the site to honor the crash victims, Boardman choked up as he called Tuesday "the worst day for me as a transportation professional." He vowed that the wrecked train and its passengers "will never be forgotten."
Federal regulators on Saturday ordered Amtrak to expand use of a speed-control system long in effect for southbound trains near the crash site to northbound trains in the same area.
Federal Railroad Administration spokesman Kevin Thompson said Sunday the automatic train control system is now fully operational on the northbound tracks. Trains going through that section of track will be governed by the system, which alerts engineers to slow down when their trains go too fast and automatically applies the brakes if the train continues to speed.
The agency also ordered Amtrak to examine all curves along the Northeast Corridor and determine if more can be done to improve safety, and to add more speed limit signs along the route.
U.S. Transportation Secretary Anthony Foxx told the 150 people present at Sunday's service that Amtrak's action on the ordered changes was one way to honor the eight passengers killed in the crash. Many were riding home to their families, he said.
"Their memories forever in our minds will fuel our work to make intercity passenger rail and our entire network in the United States stronger and safer," he said.
Almost 20 people injured in the train crash remain in Philadelphia hospitals, five in critical condition. All are expected to survive.
Investigators with the National Transportation Safety Board, meanwhile, have focused on the acceleration of the train as it approached the curve, finally reaching 106 mph as it entered the 50-mph stretch north of central Philadelphia, and only managing to slow down slightly before the crash.
"The only way that an operable train can accelerate would be if the engineer pushed the throttle forward. And ... the event recorder does record throttle movement. We will be looking at that to see if that corresponds to the increase in the speed of the train," board member Robert Sumwalt told CNN's "State of the Union."
The Amtrak engineer, who was among those injured in the crash, has told authorities that he does not recall anything in the few minutes before it happened. Characterizing engineer Brandon Bostian as extremely safety conscious, a close friend said he believed reports of something striking the windshield were proof that the crash was "not his fault."
"He's the one you'd want to be your engineer. There's none safer," James Weir of Burlison, Tennessee, told The Associated Press in a telephone interview on Sunday.
Investigators also have been looking into reports that the windshield of the train may have been struck by some sort of object, but Sumwalt said on CBS's "Face the Nation" program Sunday that he wanted to "downplay" the idea that damage to the windshield might have come from someone firing a shot at the train.
"I've seen the fracture pattern; it looks like something about the size of a grapefruit, if you will, and it did not even penetrate the entire windshield," Sumwalt said.
Officials said an assistant conductor on the derailed train said she heard the Amtrak engineer talking with a regional train engineer and both said their trains had been hit by objects. But Sumwalt said the regional train engineer recalls no such conversation, and investigators had listened to the dispatch tape and heard no communications from the Amtrak engineer to the dispatch center to say that something had struck the train.