The Kremlin's press service didn't give any reasons for Veronika Milinchuk's dismissal.
Russian media speculate she was fired because she had failed to protect Russia's interests at the court.
Her sacking came as the court ordered Russia to pay some $275,000 to the relatives of several Chechen men abducted by Russian troops in 2000 and 2002.
Russia's Prosecutor-General Yury Chaika says the court ordered Moscow to pay almost $7 million in compensation to its citizens in 2007 alone.
A successor to Milinchuk has not yet been named.