Leyla Sahin, a medical student barred from the state-run Istanbul University for wearing a headscarf, told a press conference on Wednesday that she would appeal the verdict.
"With its ruling, the European Court of Human Rights proved that it ignored Turkey's domestic, cultural structure and realities, and allowed its own abstract fears to come before the notion of justice," she said.
The Strasbourg-based court ruled on Tuesday that the state-run University had not violated her rights when it blocked her from sitting for exams in 1998 and later refused to enrol her in the faculty because of her headscarf.
The court said the headscarf ban in rigidly secular Turkey was based on the principles of secularism and equality, maintaining the ban served "for the protection of the democratic system in Turkey".
"This ruling is a disgrace for Turkey which is struggling for democracy, freedom and human rights, as well as for Europe which gives others lessons on human rights," Sahin said.
Turkish rights group Ozgur-Der (Free Thought and Educational Rights Association) called for a protest march on 1 July in Istanbul.
"This ruling of double standards will be remembered as a document of shame for human rights," said a spokesman for Ozgur-Der.
Another human rights oragnisation MAZLUM-DER (Solidarity for the oppressed) also slammed the verdict.
"The court, in fact, has damaged its own reputation and the ideal of protecting human rights on an international level," the group said in a statement.
"This ruling is a disgrace for Turkey which is struggling for democracy, freedom and human rights, as well as for Europe which gives others lessons on human rights"
Victim of headscarf ban in Turkey
"This ruling does not comply with other rulings the court has issued in the past on the subject of freedom of religion and conscience," it said.
The group also criticized the European Union, which Turkey is seeking to join, for failing to put pressure on Ankara to lift the headscarf ban.
Turkey's enforcement of the ban has been tightened since 1997 when the powerful military ousted Turkey's Islamist prime minister Necmettin Erbakan after his fight against corruption was labelled a 'danger to secularism'.
Mass protests against the ban have failed to bear fruit and, according to rights activists, an estimated 2,000 students who refuse to take off the headscarf have fallen victim to the ban and are currently being denied the right to education.