Approximately 10,000 BC, hunter-gatherer societies existed near present-day Bogotá (at "El Abra" and "Tequendama") which traded with one another and with cultures living in the Magdalena River Valley. Beginning in the first millennium BC, groups of Amerindians developed the political system of "cacicazgos" with a pyramidal structure of power headed by caciques. Within Colombia, the two cultures with the most complex cacicazgo systems were the Tayronas in the Caribbean Region, and the Muiscas in the highlands around Bogotá, both of which were of the Chibcha language family. The Muisca people are considered to have had one of the most developed political systems in South America, after the Incas.

Internal political and territorial divisions led to the secession of Venezuela and Quito (today's Ecuador) in 1830. The so-called "Department of Cundinamarca" adopted the name "Nueva Granada", which it kept until 1856 when it became the "Confederación Granadina" (Grenadine Confederation). After a two-year civil war in 1863, the "United States of Colombia" was created, lasting until 1886, when the country finally became known as the Republic of Colombia. Internal divisions remained between the bipartisan political forces, occasionally igniting very bloody civil wars, the most significant being the Thousand Days civil war (1899 - 1902) which together with the United States of America's intentions to influence in the area (especially the Panama Canal construction and control) led to the separation of the Department of Panama in 1903 and the establishment of it as a nation. Colombia was engulfed in a year-long war with Peru over a territorial dispute involving the Amazonas Department and its capital Leticia.

Soon after, Colombia achieved a relative degree of political stability, which was interrupted by a bloody conflict that took place between the late 1940s and the early 1950s, a period known as La Violencia ("The Violence"). Its cause was mainly mounting tensions between the two leading political parties, which subsequently ignited after the assassination of the Liberal presidential candidate Jorge Eliécer Gaitán on April 9, 1948. This assassination caused riots in Bogotá and became known as El Bogotazo. The violence from these riots spread throughout the country and claimed the lives of at least 180,000 Colombians. From 1953 to 1964 the violence between the two political parties decreased first when Gustavo Rojas deposed the President of Colombia in a coup d'état and negotiated with the guerrillas, and then under the military junta of General Gabriel París Gordillo.

After Rojas' deposition the two political parties Colombian Conservative Party and Colombian Liberal Party agreed to the creation of a "National Front", whereby the Liberal and Conservative parties would govern jointly. The presidency would be determined by an alternating conservative and liberal president every 4 years for 16 years; the two parties would have parity in all other elective offices. The National Front ended "La Violencia", and National Front administrations attempted to institute far-reaching social and economic reforms in cooperation with the Alliance for Progress. In the end, the contradictions between each successive Liberal and Conservative administration made the results decidedly mixed. Despite the progress in certain sectors, many social and political problems continued, and guerrilla groups were formally created such as the FARC, ELN and M-19 to fight the government and political apparatus. These guerrilla groups were dominated by Marxist doctrines.

Emerging in the late 1970s, powerful and violent drug cartels further developed during the 1980s and 1990s. The Medellín Cartel under Pablo Escobar and the Cali Cartel, in particular, exerted political, economic and social influence in Colombia during this period. These cartels also financed and influenced different illegal armed groups throughout the political spectrum. Some enemies of these allied with the guerrillas and created or influenced paramilitary groups.

In recent years, the country has continued to be plagued by the effects of the drug trade, guerrilla insurgencies like FARC and paramilitary groups such as the AUC (later demobilized, though paramilitarism remains active), which along with other minor factions have engaged in a bloody internal armed conflict. President Andrés Pastrana and the FARC attempted to negotiate a solution to the conflict between 1998 and 2002 in which the government, more or less like Pakistan negotiations with the Taliban, believed the state could not fight forever and agreed to handle huge quantity of land in return for peace. Pastrana began to implement the Plan Colombia initiative, with the dual goal of ending the armed conflict and promoting a strong anti-narcotic strategy. This strategy entailed setting a huge quantity of land as "demilitarized" zones where no soldiers from either side could reside, but as attacks from the drug cartels persisted in those zones, the government established the negotiations were ineffectual.