Imelda Cortez became pregnant at the age of 18 and denies trying to abort the baby, which is a crime under any circumstances in El Salvador.
She was taken to a hospital after giving birth and despite the child being born healthy, doctors claimed she had tried to intentionally induce an abortion.
Ms Cortez's daughter is now nearly two-years-old.
The 20-year-old will appear at court on Monday, faced with charges of attempted aggravated murder.
Judges will consider medical evidence from doctors to determine if she intentionally tried to induce an abortion.
She is one of around 25 women imprisoned in El Salvador who are accused of inducing abortions but say they actually suffered miscarriages, stillbirths or pregnancy complications, according to the Citizen Group for the Decriminalisation of Abortion (CDFA).
If convicted Ms Cortez could face up to 20 years in jail, her lawyer Alejandra Romero said.
"Imelda was repeatedly raped by her stepfather from the age of 11," he said.
"DNA tests prove her child is the daughter of her stepfather."
"Yet Imelda is being treated as a criminal, not a victim of sexual violence."
Ms Cortez's stepfather has since been jailed on charges of raping a minor.
CDFA lawyers say convictions for inducing abortions are often based on flimsy medical evidence, as it is difficult for doctors to prove if someone has tried to abort a baby.
Earlier this year, the United Nations called on El Salvador to revise its abortion law and review all such cases in which women have been jailed.
The 20-year-old's case has, regardless of the verdict, reignited debate about El Salvador's total ban on abortion.
Mariana Ardila, a lawyer at rights group Women's Link Worldwide, said judges have a duty to consider the circumstances surrounding the pregnancy, even if they find Ms Cortez guilty.
"It is crucial that the judiciary, while dispensing justice in crimes related to pregnancy, take into account the individual circumstances and background of women and girls," said Ms Ardila.
"In this case, the circumstances related to the sexual violence Imelda faced and the afterward consequences on her life."
An online petition calling on authorities to release Ms Cortez from prison has so far collected over 48,000 signatures.
Additional reporting by Reuters
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