The 249 confirmed cases of Zika on the island include 24 pregnant women.
While the newborn does not have the virus, the Health Department said it plans to continue monitoring the health of this child and other babies born to Zika-infected women for periods of up to three years.
The case of the woman who just gave birth was detected thanks to procedures established by the Puerto Rico Health Department and the U.S. Centers for Disease Control and Prevention, the statement said.
The Health Department warned earlier in March about the spread of the Zika virus across the island, where authorities fear as many as one in every five residents will be infected unless steps are taken to suppress the Aedes aegypti mosquito that carries the bug.
CDC chief Thomas Frieden, who has already traveled to Puerto Rico to appraise the threat from Zika, plans to visit the island again early next month.