The bill, which passed 228-192 mainly along partisan lines, prohibits local public stations from using federal money to pay NPR dues and buy its programs.
The prospects of support in the Democratic-controlled Senate are slim. Seven Republicans broke ranks to vote against the bill.
"It is time for American citizens to stop funding an organization that can stand on its own feet," said Rep. Doug Lamborn, R-Colo., the sponsor. He said it was not a question of content - which many conservatives say has a liberal bias - but whether taxpayer dollars should go to nonessential services. "As a country we no longer have this luxury."
Conservative antagonism toward NPR increased last week after an executive was caught on tape deriding the Tea Party movement. However, a number of Republicans denied that the measure was a vendetta against NPR.
Both the executive and the president of NPR resigned after the incident.
Democrats retorted that the legislation would do nothing to reduce the deficit and would be a blow to local public stations that rely on the national programs that include "Morning Edition" and "Wait, Wait... Don't Tell Me" to attract listeners. "This bill would pull the plug," said Rep. Ed Markey, D-Mass. "It would snuff out stations from coast to coast, many in rural areas where the public radio station is the primary source of news and information."
The White House said it "strongly opposed" the bill and voiced similar objections, saying "undercutting funding for these radio stations, notably ones in rural areas where such outlets are already scarce, would result in communities losing valuable programming, and some stations could be forced to shut down altogether."
The Associated Press contributed to this story.