Miss Hubert launched a private prosecution against two doctors who had verbally agreed to perform 'gender-abortions' in breach of the Abortion Act 1967.
The admissions were made on video during a Daily Telegraph undercover report about 'gender-abortion' in the United Kingdom, in 2012.
While the Crown Prosecution Service admitted that evidence did exist to bring a case against the two doctors, it decided it was not in the public interest to prosecute. Miss Hubert has now been ordered to pay court costs totalling £47,000.
Andrea Williams, Chief Executive of the Christian Legal Centre which is supporting Miss Hubert, commented:
"When the CPS refused to prosecute it was not because there was no evidence to convict, but because of political and policy reasons. Justice was not done here and instead Aisling, who acted upon the injustice she had witnessed, was punished.
"We argue in our application to the Strasbourg court that the statute governing private prosecutions is very clear. Costs from Aisling's case should have been drawn from the central fund which was created for cases exactly like hers.
"Both the statute and case law surrounding private prosecutions are adamant that courts must protect the right of access to these private prosecutions, by not assessing punitive costs against the person seeking justice - unless the case is frivolous, and never should have been brought.
"Just as the ruling from the Supreme Court held, access to justice in the United Kingdom must be available and affordable to all.
"In our application we note that if not for the generosity of the public, Aisling would not have been able to pay the draconian costs against her.
"We will ask the European Court to rule that that the British courts violated the European Convention of Human Rights for taking action against Aisling, because of its discriminatory views relating to abortion.
"In filing this case to the European Court, we aim to protect others like Aisling who wish to access justice and to seek private prosecutions, which provide important checks and balances.
"We also seek to ensure that no courts in the future will punish an applicant simply for seeking to defend preborn children - the most vulnerable members of our society- and wanting to stop a serious wrong from being perpetrated in breach of the law.
"We are proud to continue to stand with Aisling Hubert and hope for a positive outcome which will ensure that others like her can access justice."