The judge also said the women's detention centre that was set up in August 1992 was dubbed "The Brothel" by Serb soldiers .
The court ruled that the 37-year-old was directly and indirectly involved in the enslavement, torture, rape and killing of non-Serb civilians between April 1992 and February 1998.
The identity of the women involved was protected by the court, but it is believed that almost all of them were Muslims. Stankovic was arrested by international peacekeepers in Bosnia in 2002.
He was held in custody at The Hague-based International Criminal Tribunal for the former Yugoslavia (ICTY) until September last year, when he was sent back to Bosnia. He refused to be present in court to hear the verdict read.
Bosnian authorities are allowed to try low-profile war crimes cases, while the ICTY has the job of hearing cases involving senior wartime officials. Courts in the former Yugoslavia are expected to ease the burden of the UN tribunal, which is due to wind up its work in 2010.