Thaci said the judge in the special court of Kosovo had just informed him that the indictment against him was accepted.
"It is a very difficult moment on behalf of myself and my family, for you who believe in me and support me," he said.
He called on the citizens of Kosovo not to lose hope and to think about the freedom, independence and state formation the country has achieved in the last 30 years.
He described the indictment against him and his comrades as "a small price to pay for the freedom and construction of Kosovo."
"I resign from the post of President of the Republic of Kosovo, protecting the integrity of the Kosovo Presidency, the integrity of the Kosovo state, the integrity and dignity of the people of Kosovo, and at the same time respecting our partnership with the international community," said Thaci.
Former Kosovo Parliament Speaker and former spokesperson of the Kosovo Liberation Army (UCK) Jakup Krasniqi was detained Wednesday in a joint operation organized by the Kosovo Special Prosecutor's Office, EU Kosovo mission (EULEX) and Kosovo police.
The Kosovo Special Prosecutor's Office in The Hague announced that an indictment was also prepared against Recep Selimi, a former commander of the UCK.
The office filed an indictment on June 24 against Thaci and former Parliament Speaker Kadri Veseli on the grounds that they had committed "crimes against humanity" and "war crimes" during the 1998-99 war with Serbia.
While it was alleged that those mentioned in the indictment were responsible for the deaths of 100 people, it was reported that the suspects were also charged with war crimes such as murder, exile and torture.
Kosovo Special Prosecutor's Office and Chambers
The special court, also known as the Kosovo Special Chambers and Special Prosecutor's Office, and its private prosecutor's office were established in 2011.
The judicial body, established to investigate and try war crimes allegedly committed in the region between 1998-2000, consists of international judges and prosecutors.
The Special Prosecutor's office in The Hague, the Netherlands, has invited dozens of former UCK members to testify since the beginning of 2019.
The court also invited Ramush Haradinaj, one of Kosovo’s former prime ministers, to testify as a "suspect" in 2019, after which he resigned from his post.