The high court's judges said they could not allow a termination to the pregnancy because "abortion was neither good for the girl nor for the fetus," according to the Hindustan Times.
India has a ban on terminating pregnancies that progress beyond 20 weeks. Under India's Medical Termination of Pregnancy Act, the country doesn't allow abortion after that period unless "the termination of such pregnancy is immediately necessary to save the life of the pregnant woman."
In this case, the pregnancy was reported by the family to the police between 26th and 27th week of pregnancy, according to the victim's lawyer, Alakh Alok Srivastava, who took the case to India's Supreme court.
"So in this case when the pregnancy was reported, it was already too late," Srivastava told CNN.
He added, "That is the main problem. The problem is we cannot always blame police or court or judicial system. We also have to reflect ourselves as a family or society that where and how we failed to give adequate care and caution that was required to the child."
The girl, a resident of the Northern Indian city of Chandigarh, is eight months pregnant. She was allegedly raped repeatedly by her maternal uncle for months, according to Srivastava. The uncle has been arrested, he said.
Indira Jaising, a senior lawyer for India's Supreme Court and a leading voice on sexual assault and domestic violence, agreed that an abortion wasn't possible at this late stage.
"But the real problem is not whether an abortion is possible but whether the pregnancy can be terminated by any other means, including caesarian section," Jaising told CNN. "Allowing her to go into labor is a recipe for possible death."
She also blames the "indifference" of the medical profession.
"It is a class issue, it is an issue of access to medical services," she said. "It is an issue of access to proper information about how to deal with this situation. It is alarming that a medical professional did not attend to this much earlier."
The victim's family is extremely poor, said Srivastava.
"The girl's father is a guard, and her mother is a domestic help working in various households," Srivastava told CNN, adding that's why he took the case to the Supreme Court.
"After me taking the case, at least two things have been done: The girls will be given best medical care during pregnancy," Srivastava said.
And secondly, the court has directed the government to consider setting up permanent medical boards in every state so that they can make prompt decisions on early abortion.
"This is important because there are people who belong to the poorest section of the society and the remotest part of India," Srivastava said. "So everyone cannot travel to the Supreme Court. So the Supreme Court has asked the government to ensure every state has a permanent medical board who can make the judgment and decide abortion is permissible or not, so that people don't have to travel to the Supreme Court."
India has a grim record of sexual assaults on minors, with 20,000 cases of rape or sexual assaults reported in 2015, according to government data reported by AFP.
In May, the high court allowed a 10-year-old from the northern state of Haryana
who had been raped to abort her fetus at nearly 21 weeks into the pregnancy.