The court said yesterday the rights of the mother cannot prevail over the unborn, and vice versa.
Abortions are strictly forbidden in El Salvador. The sentence for violating the ban is 50 years in prison.
The 22 year-old woman, who gave her name only as Beatriz, is the mother of a two-year-old boy and is 25 weeks pregnant.
She was recently diagnosed with lupus, a disease that weakens her immune system, and doctors said that the fetus she carries has anencephaly, a total or partial absence of the brain and the skull.
But the Supreme Court upheld the ban on abortion, despite the dire circumstances.
Feminist groups were outraged, while Catholic organizations praised the ruling.
Salvadoran Health Minister Maria Isabel Rodriguez had asked the justices to grant Beatriz special permission to undergo the procedure, and exempt the doctors involved from any legal consequences.
The woman's mother, Maria Delmy Cortez, had published an open letter in leading newspapers asking the court to rule in favor of her daughter.
Beatriz asked to have the abortion on grounds her own life was in danger.
The case has been highly controversial. The archbishop of San Salvador, Jose Luis Escobar, asked the court several times not to allow the woman to have an abortion, arguing it would open the gates to more such requests.
Feminist groups responded saying the ruling "trampled on the right to life" of Beatriz.
"The Salvadoran state will be accountable if anything happens to Beatriz because of her high-risk pregnancy," said Ima Guirola of an association called Cemujer.
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