Aisling Hubert, 23, brought a legal challenge against doctors she accused of performing abortion on the basis of the sex of the infant.
Campaign group Christian Concern, which is supporting Ms Hubert, says she has been ordered to pay a total of £36,000 to two doctors who were filmed by a national newspaper allegedly offering abortion on the basis of the baby's gender.
She is unable to pay the bill alone, and will now face a court hearing to determine what will happen about the costs order.
A further £11,000 of costs has been awarded against Ms Hubert after an attempt to challenge the CPS' derailment of her private prosecution, bringing the total bill to £47,000.
Aisling Hubert said: "It feels as though I am being punished by the legal establishment for exposing its reluctance to challenge gender-abortion.
"These two doctors were filmed offering gender-abortion. I sought to bring them to justice. Now I am being punished and told to pay a huge sum to them. Where is the justice in that? It is completely immoral.
"This isn't just about abortion, it's about our justice system.
"Private prosecution is an important check and balance on state power. It allows private citizens to fight for justice when the state apparatus has failed or turned a blind eye.
"But these massive costs will make it impossible for people like me in the future."
Ms Hubert brought the case after a 2012 undercover newspaper investigation alleged that Manchester-based Dr Prabha Sivaraman and Birmingham-based Dr Palaniappan Rajmohan offered abortions to women who did not want to give birth to a baby they had conceived, based on the gender of the child.
Both practitioners were separately filmed offering abortion to a pregnant woman who said that she was carrying a female child but did not want to have a baby girl.
Following a police investigation the CPS decided not to proceed with the case claiming that prosecution was not in the "public interest".
