In 1994, he held the rank of captain in the Rwandan Armed Forces, and was the second-in-command, after Tharcisse Muvunyi, of the École des sous-officiers (ESO).

He was convicted of ordering the execution of Queen Dowager Rosalie Gicanda at the beginning of the killings in Butare.

Specifically, the indictment alleged that during the genocide, Nizeyimana had "instigated, encouraged, facilitated, or acquiesced to [...], the Interahamwe committing killings, kidnappings and the destruction of property.

[5] On October 6, 2009, Nizeyimana was arrested in the Ugandan capital Kampala, apparently traveling from the Democratic Republic of the Congo to Kenya on false documents.

[5] The United States government had previously offered a reward of up to US$5 million for information leading to his arrest or conviction.