Warren Kizza Besigye Kifefe was born in Rwakabengo, Rukungiri Municipality, Rukungiri District, southwestern Uganda, on 22 April 1956. He attended Kinyasano Primary School and Mbarara Junior School. The second born in a family of 6, both his parents died before he finished primary school. His father was a police man. He went to Kinyasano Primary School,and Mbarara Junior School for his Primary school education. He later joined Kampala's Kitante High School for his Ordinary Levels and then Kigezi High School in Kabale District for his Advanced Level education.
Besigye enrolled at Makerere University in 1975, graduating with a degree in human medicine in 1980. While in the bush, he became Yoweri Museveni's personal physician. When the National Resistance Movement and Army (NRM/A) came to power in January 1986, he was appointed - at the age of 29 - Minister of State for Internal Affairs. He later held the positions of Minister of State in the President's office and National Political Commissar. In 1991, he became commanding officer of the mechanised regiment in Masaka, central Uganda, and in 1993 was appointed the army's chief of logistics and engineering.
In 1998, he married Winnie Byanyima, who was the third wife of president Museveni. Byanyima, an aeronautical and mechanical engineer who worked at Uganda's high commission in the United Kingdom and served as ambassador to France in the 1980s and 1990s, is a childhood friend of Museveni's and a former member of the NRM/A who later joined the opposition. She and Besigye have one son, Anselm.
After graduating, Besigye briefly worked at Mulago National Hospital. He later went into exile in neighbouring Kenya. While there, he applied to the Medical Board for registration to work as a doctor. After getting registered, he applied for a job at the Aga Khan Hospital which he was given and then started working as a doctor and later at Kenyatta National Hospital - both in the Kenyan capital, Nairobi - before joining Museveni's rebel National Resistance Movement/Army (NRM/A) in 1982.
In 1999, Besigye wrote a document critical of the government, entitled "An Insider's View of How the NRM Lost the Broad Base". The document accused the NRM of becoming a sectarian kleptocracy and a one-man dictatorship. Besigye was charged before a court martial for "airing his views in the wrong forum". He later brokered a deal in 2000 in which the charges were dropped in exchange for an apology for publishing the document.
In October 2000, Besigye announced that he would run against Museveni in the 2001 elections. He retired from the Uganda People's Defence Forces in 2001, having attained the rank of colonel. During his campaign, Besigye, who was Museveni's strongest opponent, accused the government of widespread corruption and pushed for an end to Museveni's "Movement" system, which he said had served its purpose as an instrument in Uganda's political transition to multiparty democracy.
He lost the election, which was marred by claims of widespread vote rigging, violence and coercion of voters. In March 2001 Besigye petitioned the Supreme Court to nullify the election results. A panel of five judges voted 5-0 that there had been cheating but decided 3-2 not to annul the elections.
In June 2001, Besigye was briefly arrested and questioned by the police over allegations of treason. The government accused him of being behind a shadowy rebel group - the People's Redemption Army (PRA) - allegedly based in the Democratic Republic of the Congo (DRC). Besigye's supporters said the government had fabricated the existence of the insurgents to harm his credibility among Ugandans and the international community.
In August 2001, Besigye fled the country, citing persecution by the state. He said he was afraid for his life. He lived in South Africa for four years, during which time he continued to criticise Museveni's government. Besigye returned to Uganda on 26 October 2005, just in time to register as a voter in the 2006 elections. He was greeted by thousands and hit the campaign trail almost immediately, addressing throngs of supporters across the country. In November 2005, William Lacy Swing, the United Nations special envoy to the Great Lakes region, confirmed the existence of the PRA, naming it as one of the foreign, armed groups operating in the eastern DRC.
Besigye's campaign came to an abrupt halt on 14 November when he was arrested on charges of treason and rape. The treason charges pertained to his alleged links to the PRA and the 20-year-old northern Ugandan Lord's Resistance Army rebellion. The rape charge related to a 1997 accusation by the daughter of a deceased friend. His arrest sparked riots in Kampala and around the country. Museveni was accused of trumping up charges against his main rival in an attempt to discredit Besigye or even prevent him from standing in the election. Both the local and international community came down heavily against Museveni's administration, urging it to release Besigye on bail. The government reacted by banning all public rallies, demonstrations, assemblies or seminars related to the trial of Besigye. It further barred the media from discussing the trial, threatening media houses with the revocation of their licences should they refuse to heed the ban.
On 25 November, Uganda's high court granted Besigye bail, but he was immediately sent back to jail on military charges of terrorism and the illegal possession of weapons. Besigye denied the charges against him and has argued that as a retiree from the armed forces, he should no longer be subject to an army court martial. He was freed on bail by the high court on 6 January. Although the charges against him stand, Besigye continues to pursue his ambition to become the next president of Uganda.
The general elections of 2006 saw FDC as the main opposition party and Besigye as the main challenger against Museveni for the presidency. He stood with Miria Kalule Obote the First female Presidential candidate for the Uganda People's Congress (UPC), Abed Bwanika who stood as an independent, John Ssebana Kizito for Democratic Party (DP). Museveni was elected for another five-year tenure, having won 59% of the vote against Besigye's 37%. Besigye, who alleged fraud, rejected the result. The Supreme Court of Uganda later ruled that the election was marred by intimidation, violence, voter disenfranchisement, and other irregularities. However, the Court voted 4–3 to uphold the results of the election.
In the 2011 elections Besigye for the third time in a row lost to his main challenger, the incumbent Yoweri Museveni with a sharp decline from previous polls, failing to win in a single region. Though the election was lauded as one of the most free and fair in Ugandan history, Besigye claimed that his challenger used intimidation and rigging to win a fourth term in office.
Following his poor performance in the 2011 presidential elections, Besigye directed his party members elected to the 9th parliament to boycott it. This was rejected by the newly elected MPs, claiming that the election victory was out of their personal effort and not Besigye's or the Party, contributing to rising tensions within the FDC.
Besigye was arrested for a fourth time on 28 April, during a "walk-to-work" protest over the high prices of food and fuel. He was sprayed with pepper spray and dragged from his car by police. This was the catalyst for additional protests leading to riots across Kampala, in which at least two people were killed and 120 people wounded, leading to some 360 arrests.
Besigye opposed the re-introduction of the Uganda Anti-Homosexuality Bill into the 9th Parliament of Uganda by back bench MP David Bahati. Besigye's support of gay rights was a contentious issue in Uganda where homosexuality was already criminal under the Ugandan Penal Code (Gender References Amendment Act).
Besigye was arrested on 1 October 2012 after an attempt to make a speech to vendors in Kiseka market in Kampala, Uganda. He was taken to a central police station in the city. Earlier, police had deployed heavily at Besigye's home in a move to block him from travelling to town to hold his planned rally, but he managed to elude the security officials to a then undisclosed location until his arrest by police at the city market about an hour later.
In the 2016 elections, Besigye again stood as the FDC presidential candidate, going up against other popular candidates Amama Mbabazi and Yoweri Museveni, the President of Uganda for three decades. Besigye again lost to the Museveni, receiving only 34 percent of the vote, while Museveni won 62 percent.
In the aftermath of this election, he urged his supporters to protest peacefully against the results, claiming that the electoral process had been rigged "using intimidation of voters, imprisonment of opponents, sabotage of rallies, late delivery of election materials, delayed opening of election centers, vote falsification at undisclosed tally centers, and bribery, among other malpractices."
On May 11, 2016 he secretly swore himself in as president of Uganda, a day before the official swearing-in ceremony of President Yoweri Museveni. He was arrested by the Ugandan Army moments into his swearing in.