On 4th July 1994, Kigali fell to the RPF. The genocide finally ended in mid-July. In the resulting refugee crisis over two million Hutus fled the country.

Most have since returned, although some Hutus remained in the Democratic Republic of Congo, including some militia members that became involved in wars in the Congo. Incursions into the country by the exiled Hutu radical militia remains a concern for the government of Rwanda.

Following the end of the genocide, the RPF organised a coalition government similar to that established by President Juvénal Habyarimana in 1992. Called The Broad Based Government of National Unity, its fundamental law is based on a combination of the constitution, the Arusha accords, and political declarations by the parties. The MRND party was outlawed.

The first post-war presidential and legislative elections were held in August and September 2003, respectively. Paul Kagame received 95% of the vote in the national election which had a voter turnout of 96%. The Coalition, which includes the RPF, received 73% of the vote. The second presidential election was held in August 2010, and Paul Kagame was re-elected for a second seven-year term with 93% of the vote.

The biggest government preoccupation has been the reintegration of more than two million refugees returning to Rwanda, some for the first time since 1959; prosecuting more than 40,000 individuals detained for crimes relating to the 1994 genocide; prosecuting the many more individuals scheduled to be tried under the gacaca system; preventing the recurrence of insurgency and counterinsurgency among ex-military and Interahamwe militia; and the shift away from crisis to medium and long-term development planning.

The prison population continues to be an urgent problem, and the release of prisoners back in to the community has caused problems for survivors who face intimidation, and in some cases even murder, in reprisal action against them giving evidence at gacaca trials.

Today, Rwandans continue to struggle with the legacy of genocide and war. Rwandan genocidal leaders are on trial at the International Criminal Tribunal for Rwanda, in the Rwandan National Court system, and, most recently, through gacaca traditional courts. However survivors still seek restorative justice for the atrocities committed against them.

The current government prohibits any form of discrimination by ethnicity, race or religion. The government has also passed laws prohibiting emphasis on Hutu or Tutsi identity in most types of political activity.