Considered a Tutsi, in 1960 he and his family fled to Uganda and settled in a refugee camp in Nshungerezi, Ankole following the Rwandan Revolution of 1959 and the ouster of King Kigeli V.[1] After finishing high school in 1976, he went to Tanzania and joined the Front for National Salvation (FRONASA), a rebel group headed by Yoweri Museveni, the brother of his friend Salim Saleh.

He was regularly at the front line in northern Uganda during the new government's operations against remnants of the ousted regime as well as other rebel groups.

He was commissioned a Major General alongside Yoweri Museveni's brother Salim Saleh Akandwanaho and Elly Tumwine.

Fred Rwigyema also stands out in his contemporaries for not being involved in any war crimes while he was directing operations in Northern and North Eastern Uganda.

He was appointed Deputy Minister for Defense following the capture of power by the National Resistance Movement, but that did not take him away from directing military operations in Northern Uganda.

[8][9] However, historian Gérard Prunier states that he had established "from incontrovertible evidence (including an interview with an eyewitness to the killing)" that Rwigyema was killed by his subcommander Peter Bayingana, following an argument over tactics, and excused his readers for having accepted the "cooked version of facts [the RPF] provided" him with.