Many of the demonstrators held up posters of Sakine Cansiz, CNN reported. Cansiz, 55, was a founding member of the Kurdistan Workers Party, usually known by its Turkish acronym, PKK.
The bodies of Cansiz, Fidan Dogan and Leyla Soylemez were found Thursday in the PKK office in Paris. All three had been shot.
Turkish authorities said Saturday the bodies would be sent to Turkey for burial in their hometowns, the newspaper Hurriyet reported.
Turkish Prime Minister Recep Tayyip Erdogan suggested the three had been killed by a dissident faction in the PKK hoping to sabotage peace talks. That angered protesters, who allege they were killed by the Turkish government.
The PKK in a statement said the killers might have been from the "Turkish gladio," a coalition of paramilitary groups acting on behalf of the government, CNN said.
"It is not possible for this bloody attack to be carried out in a central place like this without the support of international intelligence services and states," the statement said.
Turkey and the United States classify the PKK as a terrorist organization. Thousands of people have been killed in the long-running conflict between Turkey and the Kurdish minority.
Erdogan asked why French President Francois Hollande met with Cansiz. Erdogan said his government notified the French through Interpol of her presence in the country, Hurriyet reported.
"The French head of state must explain why he was seeing these terrorists," Erdogan said.