The vote was 289-137, with 47 Democrats joining 242 Republicans in favor of the bill, creating a majority that could override President Barack Obama's promised veto. It also faces an uncertain future in the Senate, where Minority Leader Harry Reid said he will try to block the bill.
The high number of Democrats voting against the White House is a clear sign Obama is increasingly isolated in his position on refugees in light of the ISIS terrorist attacks on Paris.
During his trip abroad this week, Obama has offered a forceful defense of the program and derided Republican opponents as being scared of "widows and orphans."
Republicans were determined to move quickly. House Speaker Paul Ryan told reporters "this is urgent. We cannot and should not wait to act, not when our national security is at stake."
The administration's veto threat "baffles me," Ryan said, "especially given the fact that his own law enforcement top officials came to Congress and testified that there are gaps in this refugee program."
Republicans also used the debate to criticize the president's approach to fighitng terrorism.
"The real problem is ISIL and the lack of a strategy," House Majority Leader Kevin McCarthy said, adding it was "astounding" the president has yet to lay out a comprehensive approach to the threat in the Middle East.
Obama administration officials have been lobbying Democrats to oppose the measure.
FBI Director James Comey
has expressed deep concerns about the bill, two U.S. officials tell CNN. Comey has told administration and congressional officials that the legislation would make it impossible to allow any refugees into the U.S., and could even affect the ability of travelers from about three dozen countries that are allowed easier travel to the U.S. under the visa waiver program, the officials say.
There are always risks in allowing any foreigners into the U.S., Comey told the officials, adding that the FBI believes it has an effective process with intelligence and other agencies to conduct vetting of refugees.
Reid says Democrats will block bill
It is unclear when the Senate will take up the measure, but Reid on Thursday said Democrats will attempt to block it.
"We've explained here in some detail. The problem is not with refugees," Reid said when asked if Democrats could support the House bill. "I don't think we will be dealing with it over here."
Reid's language suggests Democrats will use the power of their 46 seats to block the House bill from getting the 60 votes it would need to clear procedural hurdles in the Senate.
Senate Democrats told reporters they support two measures that would respond to the Paris attacks. One would prevent people who have been to Syria or Iraq in the last five years from entering the United States through the visa waiver program. The second would prevent people on the terrorism watch list from buying guns or explosives, something currently allowed, the Democrats said.
Moves from Rand Paul, Ted Cruz
Sen. Rand Paul, R-Kentucky, is now blocking progress on a spending bill for transportation and housing programs that is currently on the floor because he is insisting on getting a vote on his amendment that is aimed at preventing Syrian refugees from entering the United States.
GOP leaders and bill managers oppose having a refugee vote on this bill because they say it is unrelated and want to deal with that issue later.
Unless the GOP presidential candidate relents, this may delay passage of the underlying funding bill until after the Thanksgiving recess when Senate Majority Leader Mitch McConnell can take the time consuming procedural steps to overcome Paul's objections.
Also Thursday, Sen. Ted Cruz attempted to quickly move two bills of his that would address the refugee laws. One bill would force Americans who join overseas terrorist groups to renounce their U.S. citizenship; a second would "immediately bar refugees" from any country "including Iraq, Libya, Somalia, Syria, or Yemen, that contains territory substantially controlled by a foreign terrorist organization," with exceptions for groups that are victims of genocide, Cruz's office said.
The bills were blocked by Democrats who denied the Texas Republican's request for unanimous consent to pass the measures.
Contentious meeting between White House and House Democrats
Earlier Thursday, White House Chief of Staff Denis McDonough and Department of Homeland Security Secretary Jeh Johnson faced strong resistance from House Democrats at a closed-door meeting. The goal was to explain how the refugee program worked, but their presentation did not "not going over well" and went "in the weeds," according to a Democratic source in the room.
This source said the "message on this is too complicated."
Virginia Democratic Rep. Gerry Connolly, who was undecided on Wednesday, attended the morning briefing with McDonough and Johnson, but voted with Republicans for the bill after reviewing the bill's details. He told reporters "the administration representatives didn't really present a compelling and cogent reason to vote no."
"If you are going to send people home Thanksgiving week, you're going to have to justify why you voted no on the only piece of legislation in front of us post Paris and it was a fairly modest bill," Connolly said.
At the meeting with House Democrats, administration officials argued that a certification process included in the bill can't be done. But several Democrats countered that the President does certifications all the time.
New York Democratic Rep. Sean Patrick Maloney told Johnson that the issue is "toxic" and the administration arguments are "insufficient."
House Democratic leaders say they did not "whip" the bill or pressure members to back the administration.
House Minority Leader Nancy Pelosi told members before the meeting to essentially vote their conscience on the bill, saying, "Nobody is asking you to do anything but listen."
Pelosi voted against the bill, saying it was a missed opportunity because Republicans didn't consult with Democrats on a bipartisan response to the Paris attacks.
"Count me as a lioness - anybody who comes near my cubs, you are dead," Pelosi said, but added the bill "sends the wrong message" about the United States' willingness to grant asylum to those fleeing war. Instead, the California Democrat argued there are more pressing issues like reforming the visa waiver program and making sure people on the terrorist watch list can't buy guns.