Born within the past two weeks, the baby suffered severe birth defects and is still in the hospital, the Associated Press reported.
Microcephaly, a birth defect where a baby is born with an abnormally small head and underdeveloped brain, was not detected in the fetus until the eighth month of pregnancy. The infant also has hearing and vision problems, Dr. Ana Rius, Puerto Rico's Secretary of Health, told the wire service.
The child will be monitored until the age of 3, the U.S. Centers for Disease Control and Prevention said Friday.
Authorities are investigating why the case was identified so late although the mother showed Zika symptoms in the first trimester of her pregnancy, Rius told the AP. She added that the mother did not receive continuous prenatal care until late in her second trimester.
There are at least five other pregnant women in Puerto Rico whose fetuses have microcephaly, Rius said. They are expected to give birth between November and January.
Zika, typically a mosquito-borne infection, was first reported in Puerto Rico last December, but the number of cases began to skyrocket this past summer.
The CDC expects a surge in the number of babies born with severe deformities in Puerto Rico in upcoming months. A recent study estimated that up to 10,300 pregnant women on the island could be infected with Zika and that between 100 to 270 babies could be born with microcephaly, the AP said.