The Justice Department filed an appeal with the Supreme Court, which is expected to announce in the coming weeks whether it will hear the case.
In delivering judgment, the panel of three Judges said Trump exceeded the limit of the authority accorded him by Congress by issuing the Executive Order.
Then, in March, Trump blasted another federal judge's ruling that blocked a revised version of the travel ban, suggesting it was a politically motivated decision that made the US look "weak". Here's a look at how the rulings compare and what might come next.
The judges, however, did not rule on whether the president's order was an unconstitutional discrimination against Muslims.
Quoting the report, it added that citizens from the countries targeted by Trump's ban are "rarely implicated in USA -based terrorism".
That violated the Constitution's prohibition on the government officially favoring or disfavoring any religion, he said. "National security is not a "talismanic incantation" that, once invoked, can support any and all exercise of executive power". Trump described the order, which replaced an earlier January 27 order that also was blocked by courts, as a "watered down, politically correct" version of his original plan.
The 9th Circuit, however, did not completely ignore the president's statements.
The judges pointed to a June 6 tweet by Trump saying the order was aimed at "dangerous countries". That helped show he was not assessing whether the six countries had ties to terrorism, they said.
Trump's initial ban called for blocking entry to all travelers native to seven Muslim nations, and for suspending America's refugee intake.
The 9th Circuit rebuffed the administration's efforts to reinstate that part of the order as well.
Attorney General Jeff Sessions said after Monday's ruling that the ban was necessary to protect national security, and the president was within his lawful authority to enact it.
This latest court room battle comes after the US Fourth Circuit Court of Appeals issued a similar decision last month which also upheld a lower court's decision blocking the ban.
The White House predicted a win at the Supreme Court.
"The President unquestionably violates that command when he issues an Order that disproportionality burdens Muslim-Americans, while denigrating the Muslim faith and making it abundantly clear that the Order's harmful effect on Muslims is far from incidental", Katyal argued.
The court could act on the administration's request as soon as later this week. A Maryland court blocked the other half of the order.
The court said the president didn't take the steps needed to justify the order, saying the president needed to make sufficient findings that the entry of people from the six designated countries and refugees would be detrimental to the interests of the U.S.
"They're considered official statements of the president of the United States", Spicer said of the president's tweets.