Simatović is, along with former head of the State Security Directorate (RDB) Jovica Stanišić being prosecuted for war crimes in Croatia and Bosnia and Herzegovina in the period from 1991-95, before the International Tribunal for the Former Yugoslavia (ICTY).

[2] On 30 June 2021, he was found guilty under counts of murder, deportation, forcible transfer and persecution as crimes against humanity that occurred during the Bosanski Šamac ethnic cleansing, and sentenced to 12 years in prison.

[9] After the assassination of Zoran Đinđić, Stanišić was arrested on 13 March 2003 during Operation Sabre by the Serbian Police and handed over to the International Criminal Tribunal for the former Yugoslavia (ICTY) on 30 May 2003.

[13] However, his acquittal as well as that of Jovica Stanišić, had been overturned on 15 December 2015 by the appeals chamber, which vacated the initial verdict deemed faulty as it was based on an insistence that the men could only be guilty if they "specifically directed" the crimes.

[23] After his provisional release ended, Simatović was returned to his UN-run detention unit and again appeared in person for an appeal hearing held at a Hague court on August 28, 2020.

[5] He was found guilty of other crimes in Bosnia and Herzegovina (Bijeljina, Zvornik, Doboj, Sanski Most, Trnovo) and Croatia (Daljska Planina), and included in a joint criminal enterprise.

[25][26] The Tribunal concluded: ...the Trial Chamber found proven beyond reasonable doubt that, from at least August 1991 and at all times relevant to the crimes charged in the Indictment, a common criminal purpose existed to forcibly and permanently remove the majority of non-Serbs from large areas of Croatia and Bosnia and Herzegovina, through the commission of the crimes of persecution, murder, deportation, and inhumane acts (forcible transfer) charged in the Indictment...

The Appeals Chamber has further concluded that all reasonable doubt has been eliminated that Stanišić and Simatović possessed the requisite mens rea for joint criminal enterprise liability.