But an EU spokesman said the ruling has no impact because the 2002 list has since been updated and still complies in terms of justifying the PKK's inclusion.
The PKK took up arms for an ethnic homeland in Turkey's southeast in 1984, sparking clashes that have killed more than 37,000 people.
'Weakens struggle'
Turkey accused the European court of undermining "anti-terror" efforts after it ruled against the EU's inclusion of a Kurdish rebel group on its list of "terrorist" organisations.
Mehmet Ali Sahin, the country's justice minister, said: "The judges were supposed to think very well before making such a ruling that weakens the international struggle against terrorism.
"I wish they had come to Turkey... and seen the threats. But, of course, they made the decision at home where there is no risk of terrorism, far from the realities."
The court's ruling follows similar judgments that the EU had failed to give sufficient reasons for including groups on the list, including exiled Iranian opposition group, the People's Mujahideen.