At least four people have died, and the government declared a state of emergency last week.
Health workers have given 160,000 vaccines in recent days, but officials say they need to administer many more.
Another health alert was declared in Paraguay last month amid a suspected outbreak of dengue fever.
Yellow fever is transmitted by infected mosquitoes and is generally confined to rural or jungle areas. The last outbreak was in 1974.
Walberto Pinanes, the director general of Vigilancia de Salud, a Paraguayan health agency, told the BBC that demand for the vaccine had exploded among fears that the outbreak was spreading.
In Luque, a suburb of the capital Asuncion and an area considered high-risk, hundreds of protesters tried to hammer down the door of a health centre, the Reuters news agency reported.
In Villa Elisa, another city close to Asuncion, residents blocked a highway and burned tires.
At least 13 people are thought to have died in an outbreak of the disease in neighbouring Brazil.