Emmanuel Rukundo (born 1 December 1959) is a Rwandan Roman Catholic priest who, in 2009, was convicted of genocide and crimes against humanity by the International Criminal Tribunal for Rwanda (ICTR) for his participation in the 1994 Rwandan Genocide.
Rukundo was also head of the St. Leon Minor Seminary in the Gitarama at the time of the 1994 Genocide.
According to findings by the ICTR, he ordered Hutu soldiers to abduct and murder Tutsi refugees who were seeking shelter at St. Leon's and, with soldiers of the Rwandan army, was responsible for abducting and killing Madame Rudahunga and severely beating two of Rudahunga's children and two other Tutsi civilians.
Rukundo was also found guilty of personally sexually assaulting a young Tutsi woman.
Rukundo fought his extradition in the Federal Supreme Court of Switzerland, but his case was dismissed and on 20 September 2001 he was sent to Arusha, Tanzania, to stand trial before the ICTR.