The refusal followed a circular from the university authorities, issued the previous month, which banned the admission of female students wearing the headscarves or male students with beards.
The European court, which upholds the European Convention on Human Rights, dismissed in June 2004 Sahin's claims that the university's decision was a violation of her freedom of thought, conscience and religion and her right to education.
It found that the university's ban on headscarves could be considered as "necessary in a democratic society" and noted that it was based on "two principles which reinforce and complement each other: secularism and equality".
In Turkey, Sahin's appeal was rejected based on the principle of secularism contained in article two of the country's constitution.
During the appeal hearing on Wednesday Sahin's lawyer, Kazim Berzeg, emphasised the fact that the head scarf was not banned in Europe and accused the judges of treating Turkey differently.
Berzeg told the hearing the European Convention on Human Rights protected the freedom of religious expression and not secularism.
No date was set for the European court's judgement on the case.