The woman, who is now 31 and known only by the initials SE, said in a statement that she was blindfolded whilst being tortured and raped.
The prosecution as a result have charged all 405 soldiers who served in two paramilitary stations in the south of the country during that period.
“In such cases it is very difficult to find the perpetrators and usually the suspects are acquitted. But even the fact that the prosecutors opened a case is something,” lawyer Eren Keskin told AFP.
Turkish authorities have shied away from investigating widespread allegations of torture and rape by security forces in the largely Kurdish southeast, which has been the location of a 15-year bloody conflict between separatist Kurdish rebels and the army.
"The present government has acknowledged that there is still much to do to bring the country in line with international human rights standards and the political criteria for accession"
Human Rights Watch
SE alleges she was tortured and raped at the hands of paramilitary troops each time she was taken into custody in November 1993 and in March and August 1994.
Her claims have been verified by a medical report.
In the last incident, she lost consciousness and came to after nine days in hospital.
SE finally sought asylum in Germany, where she is still living.
The first hearing in the case will be held on 10 October in Mardin.
Turkey's failure to stamp out torture and other human rights abuses has long impeded its bid to join the European Union.
Still, earlier this year highly respected New York-based Human Rights Watch complimented the country on repealing the death sentence in 2002 and noted a “series of symbolically and practically important reforms.”
The report continued, saying “the present government has acknowledged that there is still much to do to bring the country in line with international human rights standards and the political criteria for accession.”