Naimova, 26, tested positive at the European indoor championships in Gothenburg last March where she won the 60 metres final in a personal best time of 7.10 seconds.
She had already been banned for two years for tampering with her urine in an out-of-competition test in Sofia in 2009.
In a statement the Bulgarian federation said Naimova, who won two gold medals at the 2006 world junior championships in Beijing, would be stripped of her title and all her results between March and June would be annulled.
Ukrainian Mariya Ryemyen, who came second in Gothenburg, is the new champion with France's Myriam Soumare taking the silver medal and Bulgarian Ivet Lalova the bronze.
Naimova, who was not immediately available for comment when contacted by Reuters, can appeal to the Lausanne-based Court of Arbitration for Sport.
Bulgarian athletics has been marred by a series of doping offences in recent years.
Sprinter Inna Eftimova, middle-distance runners Daniela Yordanova, Vanya Stambolova and Teodora Kolarova, high jumper Venelina Veneva and hammer thrower Andrian Andreev have all tested positive for banned substances in the past five years.