Move following report of 1,914 new cases in the past week will allow territory access to federal funds and personnel.
The US government has declared a public health emergency in Puerto Rico as a result of a Zika epidemic.
The declaration allows the federal government to award grants, access emergency funds and temporarily appoint personnel where needed, among other things.
“This administration is committed to meeting the Zika outbreak in Puerto Rico with the necessary urgency,” Sylvia Burwell, health and human services secretary, said in a statement.
Burwell travelled to the US territory in late April to evaluate its response to the outbreak.
The announcement came just hours after Puerto Rico reported 1,914 new cases in the past week, for a total of 10,690 since the first one was reported in December.
The mosquito-borne virus has infected 1,035 pregnant women, which is a concern to authorities because Zika has been tied to a severe birth defect known as microcephaly.
More than 100 pregnant women infected with Zika in Puerto Rico who have given birth have had healthy babies, officials said.
Puerto Rico reported the first microcephaly case acquired on US soil in May, involving a dead foetus that a woman turned over to health authorities.
Since then no microcephaly cases have been reported, but federal officials said it is only a matter of time.
Puerto Rico Govenor Alejandro Garcia Padilla said he had asked federal officials to declare a public health emergency and thanked them for their support.
“Zika poses a hidden threat to future generations of Puerto Ricans, and I feel the responsibility to do everything in my power to fight the spread of it,” he said.
Garcia recently authorised the use of Bti, an organic larvicide, to fight the spread of Zika after rejecting aerial spraying with the insecticide naled as proposed by the US Centers for Disease Control and Prevention.
Ana Rius, Puerto Rico health secretary, said 90 people have been hospitalised because of Zika.
Officials also said 30 people have been diagnosed with a temporary paralysis condition known as Guillain-Barre that has been linked to Zika.
Health authorities said they believe the number of Zika cases is much higher because eight of 10 people show no symptoms and many do not go to the doctor.
The emergency was declared one day after the US surgeon general visited Puerto Rico and said he expected 25 percent of Puerto Rico’s nearly 3.5 million people will be infected with Zika by year’s end.