The virus, which is mostly spread by mosquitoes, has infected more than 23,000 people in the U.S. and its territories.
Administration officials have warned that available funds to combat Zika were close to running out. The emergency funding was seen as critical to halting the spread of the virus, whose health risks include serious birth defects, pregnancy problems and a nervous system sickness.
When it comes to advancing a vaccine, the money means candidates who are in the first phase of a vaccine trial will be able to advance into a second phase. It will also allow vaccine trials on additional candidates, federal officials said.
The Centers for Disease Control and Prevention had warned that funding for Zika would largely run out by the end of September. The agency has been using money that was originally appropriated for general emergency response needs as well as preventing a resurgence of the Ebola epidemic in West Africa.
Republicans later agreed to drop that language to win bipartisan support for the combined government funding and Zika package.
Money is needed to support mosquito control and surveillance, said Erin Sykes, a spokeswoman for the CDC. Funding is also needed to conduct multiyear studies to better understand the link between Zika and birth defects, she said, as well as new diagnostic tests for the virus.