The vote Friday was 394-1, The Washington Post reported.
The helium program has been a target of small government advocates for decades. President Ronald Reagan wanted to eliminate it and President Bill Clinton put it on his reinventing government target list -- along with aid to beekeepers and wool producers. He succeeded in killing the latter two programs but they were revived a few years later, the Post said.
Rep. Doc Hastings, R-Wash., said he agrees with those who say the helium program has had its day.
But he voted, like many others, to retain it for now because it supplies more than 40 percent of the country's helium.
"We must recognize the realities of our current situation," Hastings said.
The program costs taxpayers nothing because sales of the inert gas, used in everything from party balloons to MRI machines, pay for it.
A worldwide shortage of helium contributed to huge increases in costs for businesses that say they depend on it, the Fort Worth Star-Telegram reported in January.
The newspaper said supplies at the U.S. Federal Helium Reserve near Amarillo, where more than a third of the world's helium is produced, were running low.