It was founded through an amalgamation of other groups of Rwandan refugees in September 2000, including the former Army for the Liberation of Rwanda (ALiR), under the leadership of Paul Rwarakabije.

The FDLR made a partial separation between its military and civilian wings in September 2003 when a formal armed branch, the Forces Combattantes Abacunguzi (FOCA), was created.

Following several days of talks with Congolese government representatives, the FDLR announced on 31 March 2005 that they were abandoning their armed struggle and returning to Rwanda as a political party.

[10] On October 4, 2005, the United Nations Security Council issued a statement demanding the FDLR disarm and leave the Democratic Republic of the Congo immediately.

[11][12] In August 2007, the Congolese military announced that it was ending a seven-month offensive against the FDLR, prompting a sharp rebuke by the government of Rwanda.

Prior to this, Gen. Laurent Nkunda had split from the government, taking Banyamulenge (ethnic Tutsis in the DRC) soldiers from the former Rally for Congolese Democracy and assaulting FDLR positions, displacing a further 160,000 people.

The government of Rwanda has been hostile towards MONUC and during its proxy war with the Congo, its military forces even attacked peacekeepers while part of the CNDP.

United Nations Secretary-General Ban Ki-moon, who had made protecting civilians and combating sexual violence central themes of his presidency, was reported to be outraged by the attack.

Atul Khare, deputy head of the U.N.'s peacekeeping department, was dispatched to the region, and Margot Wallström, the organisation's special representative for sexual violence in conflict, was instructed to take charge of the U.N. response and follow up.

[24] However, in November 2009, after pressure applied by the United Nations, the German Bundeskriminalamt captured Murwanashyaka, the 46-year-old chairman of the FDLR, again, along with his 48-year-old deputy, Straton Musoni, in Karlsruhe.

The Court's judges state that there are reasonable grounds to believe that Mbarushimana bears criminal responsibility for these attacks, including murder, torture, rape, persecution and inhumane acts.

[28] On 13 July 2012, the ICC announced an arrest mandate against the FDLR chief Sylvestre Mudacumura for war crimes committed in the Kivus[29] as well as against Bosco Ntaganda.

[30] On 7 November 2019, Trial Chamber VI of International Criminal Court (ICC) sentenced Bosco Ntaganda to a total of 30 years of imprisonment.

[33] In October 2022, findings from reports by Human Rights Watch revealed that the Congolese military provided support to the FDLR in their engagement against the M23 rebel group.