The rights group says that the ban is pushing women into unsafe, clandestine abortions or forcing them to undergo dangerous pregnancies.
The constitution in the majority Roman Catholic country protects the right to life "from the moment of conception".
Women and girls who violate the ban face lengthy jail sentences.
Under El Salvador's homicide laws, women who decide to terminate their pregnancy can be sentenced to up to 50 years in prison.
"The horrific repression that women and girls in El Salvador face is truly shocking and akin to torture," says Amnesty International.
"Shockingly, the ban extends even to cases where the life of the pregnant woman is at risk, and to children who have been raped," it adds.
In May last year, a seriously ill 22-year-old woman was denied an abortion by El Salvador's Supreme Court.
The woman, referred to as Beatriz, suffered from lupus and kidney failure. The foetus had serious medical problems.
The Supreme Court upheld the Central American's nation ban, in a case that drew international attention.
A week later, doctors decided to go ahead with a premature Caesarean section, after the woman started having contractions.
The baby died five hours after the C-section.
Health Minister Maria Isabel Rodriguez said at the time that the medical intervention did not contravene the court ruling.
Amnesty International is calling on the government of El Salvador to decriminalise abortion on all counts.
El Salvador is one of seven Latin American countries where there is a total ban on abortion.
The others are Chile, the Dominican Republic, Haiti, Honduras, Nicaragua and Suriname.
El Salvador's total ban on abortions is killing women and girls and condemning others to decades in jail, says Amnesty International.