"I feel very well, because now they are going to do it," she told AFP by telephone, referring to the premature delivery that has been scheduled to take place when she is 26 weeks pregnant in a country with strict abortion laws.
The woman, 22, suffers from 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, and likely will die upon birth.
The woman, who goes by the name Beatriz, had asked to have an abortion on grounds her own life was in danger, but authorities in El Salvador -- where abortions are strictly forbidden -- refused.
On Wednesday, the Supreme Court rejected her petition to terminate the pregnancy, saying the rights of the mother cannot take precedence over those of the unborn child.
Health Minister Maria Isabel Rodriguez gave her blessing for the premature delivery, saying on Thursday that the decision to act "is in the hands of high-level doctors."
"It is very clear at this time that the pregnancy intervention is not an abortion, it is an induced birth, which is something else," Rodriguez told a news conference.
"If there's symptom that shows a serious situation, action must be taken," she said. "For me the decisive factor is protect the life of Beatriz."
Beatriz told AFP on Thursday that she was "very nervous" but wanted the Caesarean section to ensure her own health and because "the child is not going to live."
"What they did to me was not right. They made me suffer by waiting all this time here in the hospital," she said from the National Maternity Hospital in San Salvador.
She said that so far no one from the government has been in contact regarding next week's surgery, and said that that she was putting her trust "first and foremost in God" that everything will work out.
Beatriz, who is already the mother of a one-year-old son, said her mother and partner support her decision.
The sentence for violating the abortion ban is 50 years in prison.
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 meanwhile said the high court's ruling "trampled on the right to life" of Beatriz and the Inter-American Court of Human Rights (IACHR) on Thursday urged El Salvador to take "urgent measures" to protect the woman's rights.
The IACHR also called on the San Salvador government to allow Beatriz to be seen "by doctors of her choosing," and to protect the rights of her physicians treating her.