During the Burundian Civil War, the CNDD–FDD was the most significant rebel group active and became a major political party in Burundi.

The original CNDD was founded in 1994, a year after the first democratically elected President Melchior Ndadaye was killed by elements of Burundi's Tutsi-dominated army in a failed coup d'etat.

[7][8] In May 1998, Jean-Bosco Ndayikengurukiye, Nyangoma's chief of staff, caused a schism by ousting the latter over leadership issues and losses suffered by the group during the First Congo War,[9] the Nyangoma-led faction later taking a seat at the Arusha negotiations, while Ndayikengurukiye's faction carried out its fight.

[10] In 2001, the CNDD– FDD consisted of about 25,000 rebels, but in September of that year Ndayikengurukiye was ousted by a faction led by Pierre Nkurunziza over the former's handling of negotiations with the government to join the transitional administration set up by in Arusha Accords.

Months later, in the largely peaceful parliamentary elections on 4 July 2005, the CNDD–FDD won an estimated 60 to 80 percent of the vote, making it likely that a CNDD–FDD representative would be chosen the president in August.