Perihan Magden defended a conscientious objector in her weekly magazine column.
In her article, published in Yeni Aktuel magazine in December, Magden defended Mehmet Tarhan, who had been sentenced to four years in a military prison for disobedience after refusing to wear his uniform.
Magden suggested that Turkey needed to set up a civilian service as an alternative to military conscription.
In court, Magden denied that she was trying to turn people against military service.
"I only argued that conscientious objection is a human right. It is my right and duty to defend conscientious objection," she said.
Magden could be jailed for three years if convicted of "alienating the people against military service".
The trial was adjourned until July 27.
Turkish men over the age of 20 must serve in the military, and the country does not recognise the right to conscientious objection.
The military is popular in Turkey, and conscription has widespread support.
Magden, the author of Two Girls, and The Messenger Boy Murders, was jeered by onlookers as she entered the courthouse, the Anatolia news agency said.
Hansjorg Kretschmer, the EU ambassador to Turkey, said Magden's trial was "unacceptable," in a newspaper interview. "If you think there should be a right to conscientious objection in Turkey, why can't you say it? And why is this becoming a ground for prosecution?" he said.
The EU has warned Ankara that prosecuting intellectuals for exercising their right to freedom of thought could damage the country's chances of membership.
"There are many issues [in Turkey] like this which are unacceptable from a European point of view," Kretschmer said.