The 22-year-old woman, identified only as Beatriz, has severe health problems, including the autoimmune disease lupus, The New York Times reports. Her doctors say the fetus she is carrying has anencephaly, a condition in which it is missing parts of the brain and is almost certain to be stillborn or die soon after birth.
Beatriz previously gave birth to a son through a Caesarian section carried out before he was full-term.
She is in the National Maternity Hospital, waiting to learn if the Supreme Court will allow her to have an abortion in El Salvador without risking imprisonment for herself and her doctors.
"I don't want to die," she told the Times in a telephone interview. "I want to be with my boy, taking care of him."
She apparently made an appointment to be sterilized after she gave birth to her son but did not follow through, the Times said.
El Salvador is one of a handful of countries where abortion is completely illegal. The Supreme Court, which has already held a hearing on the case, is expected to rule soon.
The Catholic Church supports the strict abortion ban, saying in a statement the fetus Beatriz is carrying should not be condemned and the case "should not be used to legislate against human life."
Health Minister Maria Isabel Rodriguez urged the high court to make exceptions for cases like Beatriz's, who told the Times she believes abortion should only be allowed in extreme cases.