Historians believe that humans moved into what is now Rwanda following the last ice age, either in the Neolithic period around ten thousand years ago, or in the long humid period which followed up to around 3000 BC. Archaeological excavations have revealed evidence of sparse settlement by hunter gatherers in the late stone age, followed by a larger population of early Iron Age settlers, who produced dimpled pottery and iron tools. These early inhabitants were the ancestors of the Twa, a group of aboriginal Pygmy hunter-gatherers who remain a minority in Rwanda today. Between 700 BC and 1500 AD a series of migrations took place[clarification needed], altering the demographics of Rwanda.This led to the division of society into three groups: the Hutus, Tutsis and the original Twas.Historians have several theories regarding the origins of these groups; one theory, promoted by the German colonial authorities, is that the Tutsis were a distinct racial group, possibly of Cushitic origin and arriving after the Hutus. Others, including that of the current government, contend that the distinction was purely social.

According to oral history, the Kingdom of Rwanda was founded in the 14th or 15th centuries on the shores of Lake Muhazi. At that time it was a small state in a loose confederation with the larger and more powerful neighbours of Bugesera and Gisaka. By playing these neighbours against each other, the early kingdom flourished, expanding westwards towards Lake Kivu. In the late 16th or early 17th centuries, the Kingdom of Rwanda was invaded by the Banyoro and the kings were forced to flee westward.The formation in the 17th century of a new Rwandan dynasty by King (Mwami) Ruganzu Ndori, followed by the retaking of the Muhazi area and the conquest of Bugesera, marked the beginning of the Rwandan kingdom's dominance in the region. At its peak, the Kingdom of Rwanda extended into what is now the DRC and Uganda, reaching as far as the shores of Lake Edward.

The Berlin Conference of 1884 assigned the territory to Germany as part of Ruanda-Urundi, marking the beginning of the colonial era. It was then united with the German territory of Tanganyika to form German East Africa. Gustav Adolf von Götzen became the first European to significantly explore the country in 1894, crossing from the south-east to Lake Kivu and meeting the King. Germany then appointed a Resident for Rwanda and German missionaries and military personnel began to arrive in the country. The Germans did not significantly alter the societal structure of the country, but exerted influence by supporting the King and the existing hierarchy and placing advisers at the courts of local chiefs. They also observed and perpetuated the ethnic divisions of the country, favouring the Tutsi as the ruling class and aiding the monarchy in putting down rebellions of Hutus who did not submit to Tutsi control. In 1916, during World War I (WWI), Belgian forces defeated the Germans and took control of Ruanda-Urundi.

In 1919, following the end of WWI, the League of Nations declared Rwanda a mandate territory and asked Belgium to govern. Belgium's involvement was far more direct than that of Germany, with heavy involvement in education, health, public works, and agricultural supervision. As the population of the country grew, Belgium introduced new crops and improved agriculture techniques to try to reduce the incidence of famine, although this was unsuccessful in preventing the Ruzagayura famine of 1943-1944, which claimed the lives of up to one-third of the population.Belgium also maintained the existing class system, promoting Tutsi supremacy and disfranchising the Hutus by subjugating their northwest kingdoms into the King's central control.The Belgian authorities considered the Hutus and Tutsis different races and, in 1935, introduced identity cards labelling each individual as either Tutsi, Hutu, or Twa. This classification was often based arbitrarily on physical characteristics; borderline cases were decided on cattle ownership, with those owning ten or more cattle labelled Tutsi and others as Hutu.

Belgium continued to rule Rwanda as a UN Trust Territory after World War II, with a mandate to oversee independence.Two rival groups emerged, the Tutsi elite who favoured early independence under the existing system, and the Hutu emancipation movement led by Grégoire Kayibanda which sought an end to "Tutsi feudalism".The Belgians dropped their long-standing support for the hierarchy, favouring the Hutu party.Tension between the two groups escalated through the 1950s, culminating in the 1959 wind of destruction. Between 1959 and 1961, Hutu activists killed hundreds of Tutsis and caused more than 100,000 to become refugees in neighbouring countries. Pro-Hutu Belgian colonel Guy Logiest, High Representative in 1962, organised the first democratic elections and organized a referendum in which the country voted to abolish the monarchy. Rwanda was separated from Burundi and gained independence under Kayibanda in 1962. Cycles of violence took place during the following years, with rebel exiled Tutsis attacking from neighbouring countries and Hutus retaliating with large-scale slaughter and repression of Tutsi within Rwanda. In 1973 Juvenal Habyarimana staged a military coup and became president. During this several top-ranking officials were killed, including Kayibanda and his wife. Habyarimana claimed the government had become too corrupt, ineffective, and violent. In the years following the coup, Rwanda enjoyed relative economic prosperity and violence against Tutsis reduced, although pro-Hutu discrimination continued.

In 1990, the Rwandan Patriotic Front (RPF), a rebel group composed mostly of Tutsi refugees, invaded northern Rwanda from Uganda, initiating the Rwandan Civil War.The Rwandan government, supported by troops from France, was initially successful in suppressing the rebels, but the RPF grew in strength and by 1992 a stalemate had developed. Despite continuing ethnic strife, including Hutu displacement in the north and periodic localised extermination of Tutsi in the south, the two sides agreed a cease-fire in 1993 and negotiated a peace settlement in Arusha, Tanzania. This cease-fire ended on 6 April 1994 when Habyarimana's plane was shot down near Kigali Airport, killing the president and his Burundian counterpart. It is still unknown who launched the attack, with each side blaming the other. The shooting down of the plane served as the catalyst for the Rwandan Genocide, which began within a few hours. Over the course of approximately 100 days, between 500,000 and 1,000,000[43] Tutsi and politically moderate Hutu were killed in apparently well-planned attacks, on the orders of the interim government under the de facto control of Theoneste Bagosora[clarification needed]. The Tutsi RPF quickly restarted their offensive, and took control of the country in a slow and methodical manner, cutting off government supply routes and taking advantage of the deteriorating social order. The international response was limited, with major powers reluctant to strengthen the already overstretched UN peacekeeping force. France eventually sent troops through Operation Turquoise to create a safe area of the country, but this controversial act came too late to make a difference. The RPF took control of Kigali on 4 July and the whole country by 18 July 1994. A transitional government was sworn in with Pasteur Bizimungu as president.

The new regime faced immediate problems, with approximately two million Hutus having fled to neighbouring countries, in particular Zaire, fearing RPF reprisals for the genocide. Thousands of these died in epidemics of diseases common to refugee camps, such as cholera. The United States staged the Operation Support Hope airlift from July to September 1994 to stabilise the situation in the camps. From 1996, rising tension in eastern Zaire forced most refugees to return to Rwanda; this tension, coupled with guerrilla incursions by interahamwe militia into Rwanda fueled the country's involvement in the First and Second Congo Wars. A period of reconciliation and justice began[when?], with the establishment of the International Criminal Tribunal for Rwanda (ICTR) and the reintroduction of a traditional village court system known as Gacaca. During the 2000s the government replaced the flag, anthem and constitution, re-drew the local authority boundaries and the country joined the East African Community and the Commonwealth. Rwanda's economy and tourist numbers grew rapidly during this period.