Fossils found in Kenya suggest that primates roamed the area more than 20 million years ago. Recent findings near Lake Turkana indicate that hominids such as Homo habilis (1.8 and 2.5 million years ago) and Homo erectus (1.9 million to 350,000 years ago) are possible direct ancestors of modern Homo sapiens, and lived in Kenya in the Pleistocene epoch.

During excavations at Lake Turkana in 1984, paleoanthropologist Richard Leakey assisted by Kamoya Kimeu discovered the Turkana Boy, a 1.6-million-year-old fossil belonging to Homo erectus. Previous research on early hominids is particularly identified with Mary Leakey and Louis Leakey, who were responsible for the preliminary archaeological research at Olorgesailie and Hyrax Hill. Later work at the former site was undertaken by Glynn Isaac.

The first inhabitants of present-day Kenya were hunter-gatherer groups, akin to the modern Khoisan speakers. These people were later replaced by agropastoralist Cushitic speakers from the Horn of Africa. During the early Holocene, the regional climate shifted from dry to wetter climatic conditions, providing an opportunity for the development of cultural traditions, such as agriculture and herding, in a more favourable environment.

Around 500 BC, Nilotic-speaking pastoralists (ancestral to Kenya's Nilotic speakers) started migrating from present-day Southern Sudan into Kenya. Nilotic groups in Kenya include the Samburu, Luo, Turkana, Maasai.

By the first millennium AD, Bantu-speaking farmers had moved into the region. The Bantus originated in West Africa along the Benue River in what is now eastern Nigeria and western Cameroon. The Bantu migration brought new developments in agriculture and iron working to the region. Bantu groups in Kenya include the Kikuyu, Luhya, Kamba, Kisii, Meru, Kuria, Aembu, Ambeere, Wadawida-Watuweta, Wapokomo and Mijikenda among others.

Remarkable prehistoric sites in the interior of Kenya include the archaeoastronomical site Namoratunga on the west side of Lake Turkana and the walled settlement of ThimLich Ohinga in Migori County.

The Kenyan coast had served host to communities of ironworkers and communities of Bantu subsistence farmers, hunters and fishers who supported the economy with agriculture, fishing, metal production and trade with foreign countries. These communities formed the earliest city states in the region which were collectively known as Azania.

By the 1st century CE, many of the city-states such as Mombasa, Malindi, and Zanzibar began to establish trade relations with Arabs. This led to the increase economic growth of the Swahili states, introduction of Islam, Arabic influences on the Swahili Bantu language, cultural diffusion, as well as the Swahili city-states becoming a member of a larger trade network. Many historians had long believed that the city states were established by Arab or Persian traders, but archeological evidence has led scholars to recognize the city states as an indigenous development which, though subjected to foreign influence due to trade, retained a Bantu cultural core.

The Kilwa Sultanate was a medieval sultanate, centred at Kilwa in modern-day Tanzania. At its height, its authority stretched over the entire length of the Swahili Coast, including Kenya. It was said to be founded in the 10th century by Ali ibn al-Hassan Shirazi, a Persian Sultan from Shiraz in southern Iran. However, scholars have suggested that claims of Arab or Persian origin of city-states were attempts by the Swahili to legitimize themselves both locally and internationally. Since the 10 century, rulers of Kilwa would go on to build elaborate coral mosques and introduce copper coinage.

The Swahili built Mombasa into a major port city and established trade links with other nearby city-states, as well as commercial centres in Persia, Arabia, and even India. By the 15th-century, Portuguese voyager Duarte Barbosa claimed that "Mombasa is a place of great traffic and has a good harbour in which there are always moored small craft of many kinds and also great ships, both of which are bound from Sofala and others which come from Cambay and Melinde and others which sail to the island of Zanzibar."

Later on in the 17th century, once the Swahili coast was conquered and came under direct rule of Omani Arabs, the slave trade was expanded by the Omani Arabs to meet the demands of plantations in Oman and Zanzibar. Initially these traders came mainly from Oman, but later many came from Zanzibar (such as Tippu Tip). In addition, the Portuguese started buying slaves from the Omani and Zanzibari traders in response to the interruption of the transatlantic slave trade by British abolitionists.

Swahili, a Bantu language with Arabic, Persian, and other Middle Eastern and South Asian loanwords, later developed as a lingua franca for trade between the different peoples. Swahili now also has loan words from English.

Throughout the centuries, the Kenyan Coast has played host to many merchants and explorers. Among the cities that line the Kenyan coast is the City of Malindi. It has remained an important Swahili settlement since the 14th century and once rivalled Mombasa for dominance in the African Great Lakes region. Malindi has traditionally been a friendly port city for foreign powers. In 1414, the Chinese trader and explorer Zheng He representing the Ming Dynasty visited the East African coast on one of his last 'treasure voyages'. Malindi authorities welcomed the Portuguese explorer Vasco da Gama in 1498.

The colonial history of Kenya dates from the establishment of a German protectorate over the Sultan of Zanzibar's coastal possessions in 1885, followed by the arrival of the Imperial British East Africa Company in 1888. Imperial rivalry was prevented when Germany handed its coastal holdings to Britain in 1890. This was followed by the building of the Kenya–Uganda railway passing through the country.

The building of the railway was resisted by some ethnic groups—notably the Nandi led by Orkoiyot Koitalel Arap Samoei for ten years from 1890 to 1900—however the British eventually built the railway. The Nandi were the first ethnic group to be put in a native reserve to stop them from disrupting the building of the railway.

During the railway construction era, there was a significant inflow of Indian people, who provided the bulk of the skilled manpower required for construction. They and most of their descendants later remained in Kenya and formed the core of several distinct Indian communities such as the Ismaili Muslim and Sikh communities.

While building the railway through Tsavo, a number of the Indian railway workers and local African labourers were attacked by two lions known as the Tsavo maneaters.

At the outbreak of World War I in August 1914, the governors of British East Africa (as the protectorate was generally known) and German East Africa agreed a truce in an attempt to keep the young colonies out of direct hostilities. Lt. Col. Paul von Lettow-Vorbeck took command of the German military forces, determined to tie down as many British resources as possible. Completely cut off from Germany, von Lettow conducted an effective guerrilla warfare campaign, living off the land, capturing British supplies, and remaining undefeated. He eventually surrendered in Northern Rhodesia (today Zambia) fourteen days after the Armistice was signed in 1918.

To chase von Lettow, the British deployed the British Indian Army troops from India but needed large numbers of porters to overcome the formidable logistics of transporting supplies far into the interior on foot. The Carrier Corps was formed and ultimately mobilised over 400,000 Africans, contributing to their long-term politicisation.

In 1920, the East Africa Protectorate was turned into a colony and renamed Kenya for its highest mountain.

During the early part of the 20th century, the interior central highlands were settled by British and other European farmers, who became wealthy farming coffee and tea. (One depiction of this period of change from one colonist's perspective is found in the memoir Out of Africa by Danish author Baroness Karen von Blixen-Finecke, published in 1937.) By the 1930s, approximately 30,000 white settlers lived in the area and gained a political voice because of their contribution to the market economy.

The central highlands were already home to over a million members of the Kikuyu people, most of whom had no land claims in European terms and lived as itinerant farmers. To protect their interests, the settlers banned the growing of coffee, introduced a hut tax, and the landless were granted less and less land in exchange for their labour. A massive exodus to the cities ensued as their ability to provide a living from the land dwindled. There were 80,000 white settlers living in Kenya in the 1950s.

Throughout World War II, Kenya was an important source of manpower and agriculture for the United Kingdom. Kenya itself was the site of fighting between Allied forces and Italian troops in 1940–41 when Italian forces invaded. Wajir and Malindi were bombed as well.

In 1952, Princess Elizabeth and her husband Prince Philip were on holiday at the Treetops Hotel in Kenya when her father, King George VI, died in his sleep. The young princess cut short her trip and returned home immediately to take her throne. She was crowned Queen Elizabeth II at Westminster Abbey in 1953 and as British hunter and conservationist Jim Corbett (who accompanied the royal couple) put it, she went up a tree in Africa a princess and came down a queen.

Mau Mau Uprising (1952–1959)

From October 1952 to December 1959, Kenya was in a state of emergency arising from the Mau Mau rebellion against British rule. The Mau Mau, also known as the Kenya Land and Freedom Army, were primarily members of the Kikuyu Group.

The governor requested and obtained British and African troops, including the King's African Rifles. The British began counter-insurgency operations. In May 1953, General Sir George Erskine took charge as commander-in-chief of the colony's armed forces, with the personal backing of Winston Churchill.

The capture of Warũhiũ Itote (also known as General China) on 15 January 1954 and the subsequent interrogation led to a better understanding of the Mau Mau command structure. Operation Anvil opened on 24 April 1954, after weeks of planning by the army with the approval of the War Council. The operation effectively placed Nairobi under military siege. Nairobi's occupants were screened and the Mau Mau supporters moved to detention camps. The Home Guard formed the core of the government's strategy as it was composed of loyalist Africans, not foreign forces such as the British Army and King's African Rifles. By the end of the emergency, the Home Guard had killed 4,686 Mau Mau, amounting to 42% of the total insurgents.

The capture of Dedan Kimathi on 21 October 1956 in Nyeri signified the ultimate defeat of the Mau Mau and essentially ended the military offensive. During this period, substantial governmental changes to land tenure occurred. The most important of these was the Swynnerton Plan, which was used to both reward loyalists and punish Mau Mau.

The first direct elections for native Kenyans to the Legislative Council took place in 1957. Despite British hopes of handing power to "moderate" local rivals, it was the Kenya African National Union (KANU) of Jomo Kenyatta that formed a government. The Colony of Kenya and the Protectorate of Kenya each came to an end on 12 December 1963 with independence being conferred on all of Kenya. The United Kingdom ceded sovereignty over the Colony of Kenya. The Sultan of Zanzibar agreed that simultaneous with independence for the Colony of Kenya, the Sultan would cease to have sovereignty over the Protectorate of Kenya so that all of Kenya would be one sovereign, independent state. In this way, Kenya became an independent country under the Kenya Independence Act 1963 of the United Kingdom. Exactly 12 months later on 12 December 1964, Kenya became a republic under the name "Republic of Kenya".

Concurrently, the Kenyan army fought the Shifta War against ethnic Somali rebels inhabiting the Northern Frontier District, who wanted to join their kin in the Somali Republic to the north. A cease fire was eventually reached with the signature of the Arusha Memorandum in October 1967, but relative insecurity prevailed through 1969. To discourage further invasions, Kenya signed a defence pact with Ethiopia in 1969, which is still in effect.

On 12 December 1964 the Republic of Kenya was proclaimed, and Jomo Kenyatta became Kenya's first president.

Moi era (1978–2002)

At Kenyatta's death in 1978, Daniel arap Moi became President. Daniel arap Moi retained the Presidency, being unopposed in elections held in 1979, 1983 (snap elections) and 1988, all of which were held under the single party constitution. The 1983 elections were held a year early, and were a direct result of an abortive military coup attempt on 2 August 1982.

The abortive coup was masterminded by a low ranked Air Force serviceman, Senior Private Hezekiah Ochuka, and was staged mainly by enlisted men in the Air Force. The putsch was quickly suppressed by forces commanded by Chief of General Staff Mahamoud Mohamed, a veteran Somali military official. They included the General Service Unit (GSU)—a paramilitary wing of the police—and later the regular police.

On the heels of the Garissa Massacre of 1980, Kenyan troops committed the Wagalla massacre in 1984 against thousands of civilians in Wajir County. An official probe into the atrocities was later ordered in 2011.

The election held in 1988 saw the advent of the mlolongo (queuing) system, where voters were supposed to line up behind their favoured candidates instead of a secret ballot. This was seen as the climax of a very undemocratic regime and it led to widespread agitation for constitutional reform. Several contentious clauses, including one that allowed for only one political party, were changed in the following years. In democratic, multiparty elections in 1992 and 1997, Daniel arap Moi won re-election.

2000s

In 2002, Moi was constitutionally barred from running, and Mwai Kibaki, running for the opposition coalition "National Rainbow Coalition" (NARC), was elected President. Anderson (2003) reports the elections were judged free and fair by local and international observers, and seemed to mark a turning point in Kenya's democratic evolution.

In 2005, Kenyans rejected a plan to replace the 1963 independence constitution with a new one.

The toll of the 2007 Post-election violence included approximately 1,500 deaths and up to 600,000 people left internally displaced.

In mid-2011, two consecutive missed rainy seasons precipitated the worst drought in East Africa seen in 60 years. The northwestern Turkana region was especially affected, with local schools shut down as a result. The crisis was reportedly over by early 2012 because of coordinated relief efforts. Aid agencies subsequently shifted their emphasis to recovery initiatives, including digging irrigation canals and distributing plant seeds.