Trump said he's ready to take this fight in his words: "Through the system."
The hearing, which was conducted by phone, started with the federal judges pressing the DOJ for evidence that would justify reinstating the order, which curtailed immigrants and refugees from seven majority Muslim countries and banned Syrian asylum seekers indefinitely.
"The president determined that there was a real risk" of terrorism and determined that the "visa screening procedures are crucial," said August E. Flentje, special counselor arguing on behalf of the Justice Department. Federal authorities determined that the seven countries covered by the order "posed the greatest threat for terrorism," Flentje said.
Flentje, seeking a stay of a temporary restraining order granted by a Washington federal court, repeated the administration's argument that the order was not a Muslim ban and that the statements indicating it was were just "newspaper articles."
But Judge Richard Clifton also cited statements by Trump's advisers, including former New York City mayor Rudy Giuliani, and asked if Flentje denied that they were made. "Now, if they were made but not to be a serious policy principle, I understand that," Clifton said. "But if it were made, it is potential evidence and a basis for an argument."
Protesters say they won't give up their fight. "I'm very proud to stand with people who are Muslim, who are not Muslim, who have no faith whatsoever, together in opposition, and to resist," Oakland resident Paul Paz said.
Judges William Canby, Clifton and Michelle Friedland sharply questioned the lawyers arguing Trump's travel ban.
The attorney representing the president was asked if there really is a risk to national security.
Friedland asked: "Has the government pointed to any evidence connecting these countries with terrorism?"
"In 2015 and 2016 both Congress and the administration made determinations," Flentje said.
Opponents of the travel ban say it is discriminatory and is causing harm to immigrants. "We had students and faculty at our state universities stranded overseas, we had families that were separated," Washington Solicitor General Noah G. Purcell said.
He was also questioned about the security risk.
"Do you deny that in fact there is concern about people coming from those countries?" Clifton asked.
"Congress and the executives had determined that those countries should not get a waiver from a Visa requirement. That is imminently different from a complete ban," Purcell said.
John Trasvina, dean of the law school at the University of San Francisco listened to the arguments and believes the judges seem to be leaning against Trump. "They're leaning in favor of the state of Washington's arguments, about the harm that is caused by the executive order and the lack of harm demonstrated by having a temporary restraining order," Trasvina said.
The judges are expected to make their decisions later this week.
Click here for more stories and videos about President Trump.
ABC News contributed to this story.