In 1948 the assassination of populist Jorge Eliécer Gaitán radically stirred up the armed conflict. It led to the Bogotazo, an urban riot killing more than 4,000 people, and subsequently to ten years of sustained rural warfare between members of Colombian Liberal Party and the Colombian Conservative Party, a period known as La Violencia ("The Violence"), which took the lives of more than 200,000 people throughout the countryside.

In October 1959, the United States sent a "Special Survey Team", composed of counterinsurgency experts, to investigate Colombia's internal security situation.

In February 1962, a Fort Bragg top-level U.S. Special Warfare team headed by Special Warfare Center commander General William P. Yarborough, visited Colombia for a second survey.

In the early 1960s Colombian Army units loyal to the National Front began to attack peasant communities. This happened throughout Colombia with the Colombian army considering that these peasant communities were enclaves for bandits and Communists. It was the 1964 attack on the community of Marquetalia that motivated the later creation of FARC.

By 1974, another challenge to the state's authority and legitimacy had come from the 19th of April Movement (M-19), leading to a new phase in the conflict. The M-19 was a mostly urban guerrilla group, founded in response to an electoral fraud during the final National Front election of Misael Pastrana Borrero (1970–1974) and the forced removal of former president Gustavo Rojas Pinilla.

Guerrillas and newly wealthy drug lords had mutually uneven relations and thus numerous incidents occurred between them. Eventually the kidnapping of drug cartel family members by guerrillas led to the creation of the 1981 Muerte a Secuestradores (MAS) death squad ("Death to Kidnappers").

Pressure from the U.S. government and critical sectors of Colombian society was met with further violence, as the Medellín Cartel and its hitmen, bribed or murdered numerous public officials, politicians and others who stood in its way by supporting the implementation of extradition of Colombian nationals to the U.S. Victims of cartel violence included Justice Minister Rodrigo Lara Bonilla, assassinated in 1984, an event which made the Betancur administration begin to directly oppose the drug lords.

The first negotiated cease-fire with the M-19 ended when the guerrillas resumed fighting in 1985, claiming that the cease-fire had not been fully respected by official security forces, saying that several of its members had suffered threats and assaults, and also questioning the government's real willingness to implement any accords.

The Betancur administration in turn questioned the M-19's actions and its commitment to the peace process, as it continued to advance high-profile negotiations against with the FARC, which led to the creation of the Patriotic Union (Unión Patriótica) -UP-, a legal and non-clandestine political organization.

On November 6, 1985, the M-19 stormed the Colombian Palace of Justice and held the Supreme Court magistrates hostage, intending to put president Betancur on trial. In the ensuing crossfire that followed the military's reaction, some 120 people lost their lives, as did most of the guerrillas, including several high-ranking operatives and 12 Supreme Court Judges. Both sides blamed each other for the outcome. This marked the end of Betancur's peace process.

In June 1987, the ceasefire between FARC and the Colombian government formally collapsed after the guerrillas attacked a military unit in the jungles of Caquetá.

In October 1987, the UP's 1986 presidential candidate Jaime Pardo Leal was assassinated amid a wave of violence that would lead to the deaths of thousands of its party members at the hands of death squads. According to Pecáut, the killers included members of the military and the political class who had opposed Belisario Betancur's peace process and considered the UP to be little more than a "facade" for FARC, as well as drug traffickers and landowners who were also involved in the establishment of paramilitary groups.

The M-19 and several smaller guerrilla groups were successfully incorporated into a peace process as the 1980s ended and the '90s began, which culminated in the elections for a Constituent Assembly of Colombia that would write a new constitution, which took effect in 1991.

Paramilitary activities increased, both legally and illegally. The creation of legal CONVIVIR self-defense and intelligence gathering groups was authorized by Congress and the Samper administration in 1994.

In mid-1996, a civic protest movement made up of an estimated 200,000 coca growers from Putumayo and part of Cauca began marching against the Colombian government to reject its drug war policies, including fumigations and the declaration of special security zones in some departments.

In Las Delicias, Caquetá, five FARC fronts (about 400 guerrillas) recognized intelligence pitfalls in a Colombian Army base and exploited them to overrun it on August 30, 1996, killing 34 soldiers, wounding 17 and taking some 60 as prisoners.

In the past, the Colombian government laid landmines around 34 military bases to protect key infrastructure, but it renounced their use in 1997.

Members of CONVIVIR groups were accused of committing numerous abuses against the civilian population by several human rights organizations. The groups were left without legal support after a 1997 decision by the Colombian Constitutional Court which restricted many of their prerogatives and demanded stricter oversight.

In April 1997, preexisting paramilitary forces and several former CONVIVIR members were joined to create the AUC (United Self-Defense Forces of Colombia), a large paramilitary militia closely tied to drug trafficking which carried out attacks on the FARC and ELN rebel groups as well as civilians starting with the 1997 Mapiripán Massacre.

The Samper administration reacted against FARC's attacks by contacted the guerrillas in order to negotiate the release of some or all of the hostages in FARC hands, which led to the temporary demilitarization of the municipality of Cartagena del Chairá, Caquetá in July 1997 and the unilateral liberation of 70 soldiers, a move which was opposed by the command of the Colombian military. Other contacts between the guerrillas and government, as well as with representatives of religious and economic sectors, continued throughout 1997 and 1998.

A New Significant attack took place in El Billar, Caquetá on March 2, 1998, where a Colombian Army counterinsurgency battalion was patrolling, resulting in the death of 62 soldiers and the capture of some 43.

On August 7, 1998, Andrés Pastrana Arango was sworn in as the President of Colombia. A member of the Conservative Party, Pastrana defeated Liberal Party candidate Horacio Serpa in a run-off election marked by high voter turn-out and little political unrest. The new president's program was based on a commitment to bring about a peaceful resolution of Colombia's longstanding civil conflict and to cooperate fully with the United States to combat the trafficking of illegal drugs.

In July 1999, Colombian military forces attacked the town of Puerto Lleras, Colombia where FARC rebels were stationed. Using U.S. supplied aircraft and equipment, and backed with U.S. logistical support, Colombian government forces strafed and bombed the town for over 72 hours.

In 2001 the largest government supported paramilitary group, the AUC, which had been linked to drug trafficking and attacks on civilians, was added to the US State Department's list of Foreign Terrorist Organizations and the European Union and Canada soon followed suit.

On January 17, 2002, right-wing paramilitaries entered the village of Chengue, and divided up the villagers into two groups. They then went from person to person in one of the groups, smashing each person's head with sledgehammers and rocks, killing 24 people, as the Colombian military sat by and watched. Two other bodies were later discovered dumped in a shallow grave. As the paramilitaries left, they set fire to the village.

Colombian authorities indicated that a boy matching Emmanuel's description had been taken to a hospital in San José del Guaviare in June 2005. The child was in poor condition; one of his arms was hurt, he had severe malnutrition, and he had diseases that are commonly suffered in the jungle. Having been evidently mistreated, the boy was later sent to a foster home in Bogotá and DNA tests were announced in order to confirm his identity.

Starting in 2004 a disarmament process was begun of Colombia's paramilitary groups (especially the AUC) and was completed on April 12, 2006, when 1,700 fighters turned in their weapons in the town of Casibare.

In May 2006, the Colombian presidential election resulted in Uribe winning re-election with a historic first round vote tally of 62%, followed by leftist Carlos Gaviria with 22% and Horacio Serpa.

On June 28, 2007 the FARC suddenly reported the death of 11 of the 12 kidnapped provincial deputies from Valle del Cauca Department. The Colombian government accused the FARC of executing the hostages and stated that government forces had not made any rescue attempts. FARC claimed that the deaths occurred during a crossfire, after an attack to one of its camps by an "unidentified military group".

At the end of 2007, FARC agreed to release former senator Consuelo González, politician Clara Rojas and her son Emmanuel, born in captivity after a relationship with one of her captors. Operation Emmanuel was proposed and set up by Venezuelan President Hugo Chávez, with the permission of the Colombian government. The mission was approved on December 26. Although, on December 31, FARC claimed that the hostage release had been delayed because of Colombian military operations. On the same time, Colombian President Álvaro Uribe indicated that FARC had not freed the three hostages because Emmanuel may not be in their hands anymore. Two FARC gunmen were taken prisoner.

On January 4, 2008, the results of a mitochondrial DNA test, comparing the child's DNA with that of his potential grandmother Clara de Rojas, were revealed by the Colombian government. It was reported that there was a very high probability that the boy was indeed part of the Rojas family.The same day, FARC released a communique in which they admitted that Emmanuel had been taken to Bogotá and "left in the care of honest persons" for safety reasons until a humanitarian exchange took place. The group accused President Uribe of "kidnapping" the child in order to sabotage his liberation.

on January 10, 2008, FARC released Rojas and Gonzalez through a humanitarian commission headed by the International Committee of the Red Cross.

On January 13, 2008, Venezuelan President Hugo Chávez stated his disapproval with the FARC strategy of armed struggle and kidnapping saying "I don't agree with kidnapping and I don't agree with armed struggle".

On February 2008, FARC released four political hostages "as a gesture of goodwill" toward Chávez, who had brokered the deal and sent Venezuelan helicopters with Red Cross logos into the Colombian jungle to pick up the freed hostages.

On March 1, 2008, the Colombian armed forces launched a military operation 1.8 kilometres into Ecuador on a FARC position, killing 24, including Raúl Reyes, member of the FARC Central High Command. This led to the 2008 Andean diplomatic crisis between Colombia and Ecuadorian President Rafael Correa, supported by Venezuelan President Hugo Chávez.

On March 3, Iván Ríos, also a member of the FARC Central High Command was killed by his security chief "Rojas". In March 2008 alone, FARC lost 3 members of their Secretariat, including their founder.

In May 2008, a dozen jailed paramilitary leaders were extradited to the United States on drug-related charges.

On May 24, 2008, Colombian magazine, Revista Semana, published an interview with Colombian defense minister Juan Manuel Santos in which Santos mentions the death of Manuel Marulanda Vélez. The news was confirmed by FARC-commander 'Timochenko' on Venezuelan based television station Telesur on May 25, 2008. 'Timochenko' announced the new commander in chief is 'Alfonso Cano'.

On July 2, 2008, the Colombian armed forces launched Operation Jaque that resulted in the freedom of 15 political hostages, including former Colombian presidential candidate Íngrid Betancourt, Marc Gonsalves, Thomas Howes, and Keith Stansell, three American military contractors employed by Northrop Grumman and 11 Colombian military and police. Two FARC members were arrested. This trick to the FARC was presented by the Colombian government as a proof that the guerrilla organisation and influence is declining.

On October 26, 2008, after 8 years of captivity, the ex-congressman Óscar Tulio Lizcano escaped with the assistance of a FARC rebel he convinced to travel with him.

In February 2009, the guerrilla released 6 hostages as a humanitarian gesture.

In March, the guerrilla released Swedish hostage Erik Roland Larsson.

In April 2009, the Colombian armed forces launched Strategic Leap, an offensive in borders areas where the FARC's forces still has a strong military presence, especially in Arauca, near the Venezuelan border.

In November 2009, Nine Colombian soldiers were killed when their post was attacked by FARC guerrillas in a southwestern part of the country.

On December 22, 2009, FARC rebels raided the home of Provincial governor Luis Francisco Cuéllar, killing one police officer and wounding two. Cuellar was found dead the following day.

On January 1, 2010, Eighteen FARC rebels were killed when the Colombian Air Force bombed a jungle camp in Southern Colombia. Colombian troops of the elite Task Force Omega then stormed the camp, capturing fifteen FARC rebels, as well as 25 rifles, war materials, explosives, and information which was given to military intelligence. In Southwestern Colombia, FARC rebels ambushed an army patrol, killing a soldier. The troops then exchanged fire with the rebels. During the fighting, a teenager was killed in the crossfire.

When Juan Manuel Santos was elected president in August 2010, he promised to "continue the armed offensive" against rebel movements. In the month after his inauguration, FARC and ELN killed roughly 50 soldiers and policemen in attacks all over Colombia.

In September 2010, the FARC's second-in-command Mono Jojoy was killed. By the end of 2010, it became increasingly clear that "neo-paramilitary groups", referred to as "criminal groups" (BACRIM) by the government, had become an increasing threat to national security, with violent groups such as Los Rastrojos and Aguilas Negras taking control of large parts of the Colombian countryside.

In 2011, the Colombian Congress issued a statement claiming that the FARC has a "strong presence" in roughly one third of Colombia, while their attacks against security forces "have continued to rise" throughout 2010 and 2011.

In 2012, the Colombia Military launched The Espada de Honor War Plan, an aggressive counterinsurgency strategies that aims to dismantle FARC's structure, crippling them both militarily and financially. The plan targets FARC leadership and it is focused on eliminating 15 of the most powerful economic and military fronts.

On July 20, 2013, as peace talks were making progress, two rebel attacks on government positions killed 19 soldiers and an unspecified number of combatants. It was the deadliest day since peace talks began in November 2012.

In December 2013, The Washington Post revealed a covert CIA program, started in the early 2000s, which provides the Colombian government with intelligence and GPS guidance systems for smart bombs.

On 15 December 2014, 9 FARC guerrillas were killed in the aftermath airstrikes conducted by the Colombian air force in the Meta province.

In March 2015, FARC stated that it would begin humanitarian demining in selected parts of Colombia.

On 22 May 2015, the FARC suspended a truce after 26 of its fighters were killed in a government air and ground offensive.

On 22 June 2015, a Colombian Army Black Hawk helicopter was destroyed while landing on a mine field laid by FARC: four soldiers were killed and six were wounded.

On 23 June 2016, the Colombian government and FARC agreed to a ceasefire.

A "final, full and definitive accord" was agreed to on August 24, 2016. This accord does not include ELN.

On 2 October 2016, the results of the referendum to decide whether or not to support the peace accord showed that 50.2% opposed the accord while 49.8% favoured it.

In October 2016, President Juan Manuel Santos was awarded the Nobel Peace Prize for his resolute efforts to bring the country's more than 50-year-long war to an end.

The Colombian government and the FARC on November 24 signed a revised peace deal and the revised agreement will be submitted to Congress for approval. The House of Representatives unanimously approved the plan on November 30, a day after the Senate also gave its backing.

FARC dissidents are a group formerly part of the Revolutionary Armed Forces of Colombia, who have refused to lay down their arms after the FARC-government peace treaty came into effect in 2016. On 15 July 2018, the Colombian and Peruvian governments launched a joint military effort known as Operation Armageddon to combat FARC dissidents. Peru issued a 60-day state of emergency in the Putumayo Province, an area bordering both Colombia and Ecuador. On the first day alone, more than 50 individuals were arrested in the operation, while four cocaine labs were dismantled. The group has attempted to recruit locals in the Putumayo Province in Peru to take up their cause.

On April 25, senior Gulf's Cartel (Clan de Golfo) leader Gustavo Adolfo Álvarez Téllez, who was one of Colombia's most-wanted drug lords and had the bounty of up to 580 million pesos for his capture, was arrested at his lavish estate in Cereté while holding a party under quarantine during the COVID-19 pandemic. Álvarez was described as the "brain" of the cartel, and by this point was reported to have taken charge of the cartel's Caribbean operations.

On June 26, Clan del Golfo and FARC dissidents were confirmed to be in a direct armed conflict in northern Antioquia known as Operation Mil. The Gulf's Clan, which dispatched 1,000 of its paramilitaries from Urabá, southern Córdoba, and Chocó, hopes to remove FARC dissent from northern Antioquia and take control of the entire municipality of Ituango.