Savisaar was born to Estonian father Elmar Savisaar and ethnic Russian (from Petseri County) mother Maria Burešin, who lived in Vastse-Kuuste. In 1949 his parents wanted to leave the local kolkhoz with their livestock, this resulted in a physical conflict. Both were arrested on charges of seizing public property, tax evasion and an assault. Elmar Savisaar was sentenced 15 years (freed in 1952) and Marie Burešin 5 years (freed in 1950) in prison.
Marie Savisaar gave birth to Edgar Savisaar in Harku women's prison while serving the sentence. The mother with the newborn was released the same year after being pardoned and they returned to Vastse-Kuuse.
After graduating from high school, Savisaar continued his studies at the University of Tartu. In 1973, he graduated from the university with a degree in history. In 1980, he wrote his candidate thesis in philosophy on the topic "Social Philosophical Foundations of the Global Models of the Club of Rome".
From 1980 to 1988, Savisaar worked in the Soviet Estonian governmental institutions dealing with the planning of economy. During 1988–1989, he was the academic director for the consultation company "Mainor".
In April he co-established the Popular Front (Rahvarinne) which became the first political mass organization in Soviet Union outside Communist Party after 1920. Initially formed to "support perestroika" Popular Front started increasingly develop ideas of Estonian national independence and created so called Singing Revolution phenomenon. The process with several others lead to dissolution of Soviet Union ultimately.
In 1989, he became the Vice-Chairman of the Council of Ministers of Estonian SSR and the Head of the State Plan Committee. In 1990, he was the Minister of Economic Affairs. On 3 April 1990, he was appointed the Chairman of the Council of Ministers. When Estonia declared its independence on 20 August 1991, he became the first Prime Minister of the Republic of Estonia. His government was in office until 29 January 1992, when he resigned after supplementary problems and a continuing decline in economy.
From 1992 until 1995, Savisaar was the Vice-Speaker of the Estonian Parliament (Riigikogu). From 17 April – 6 November 1995, he was the Minister for Internal Affairs. When he was accused of recording private conversations of other politicians, the entire government faltered. Although his participation in the recordings was never proved, he announced his intention to leave politics. However, in 1996, he participated in the elections of the Riigikogu and became the Chairman of the Tallinn City Council. His return to the Centre Party leader's post evoked a split, as some leading members disillusioned with Savisaar's leadership style left to found Arengupartei. From 2001 to 14 October 2004, he was mayor of Tallinn. On 11 April 2005, he became Minister of Economic Affairs and Communications in the new coalition of Prime Minister Andrus Ansip and worked in the post until March 2007. From 2007 he has been mayor of Tallinn, the capital of Estonia.
Edgar Savisaar and Estonia People's Union leader Villu Reiljan jointly supported Arnold Rüütel's candidature for presidency in August–September 2006; Toomas Hendrik Ilves was elected though, a choice criticised by Savisaar and attributed by him to alleged hostile media and partisan lawmakers. Savisaar refused to congratulate the winner.
In 2016, the discussion on electing a new leader escalated in the Centre Party and an extraordinary party congress was called for November. MP Jüri Ratas was the first to announced his candidacy, after which four others followed, including Yana Toom. Even though Savisaar first announced his candidacy, he later announced that he would not participate the leadership election and instead endorsed Toom.
Savisaar has published four books. He has received the Order of the National Coat of Arms 2nd Class in 2001 and 1st Class in 2006 from Estonia and the Order of the Three Stars 2nd Class in 2005 from Latvia.
Savisaar is one of the most controversial politicians in Estonia. While some people, including many from the Russian-speaking minority, see him as a defender of the poor, his political opponents accuse him of authoritarianism, nepotism, corruption, destructive intrigues, and having close ties with some Russian politicians. The latter accusation has been fuelled by the Centre Party's collaboration agreement with Putin's United Russia party, particularly since the agreement's content has not been made public. Savisaar is often associated with using Machiavellian politics and deals to achieve his goals, such as taping other politicians, which caused the so-called tape scandal in 1995; and while being the mayor of the Estonian capital Tallinn, real-estate deals that were good for the members of the Centre Party, but were bad for the town.
During the events surrounding the Bronze Soldier, Edgar Savisaar spoke out against the removal of the monument and accused Andrus Ansip of deliberate attempts of splitting the Estonian society by provoking the Russian minority. In response to this many government officials and public figures have stated distrust and disrespect towards him.
In relation to his reactions to the Bronze Soldier controversy, the Estonian Patriotic Movement created on 29 April 2007 an online petition website www.mahasavisaar.com to suggest resignation of Savisaar's position as the Mayor of Tallinn. It ended on the 9 May 2007 and had collected 98,200 e-mail addresses (not signatures, although organizers of petition claimed so). In 2009 being a candidate for EP elections collected a 103506 votes in closed list system.
On 17 July 2015, Estonian Internal Security Service launched a criminal investigation on Savisaar and six others in relation to bribery allegations. He is suspected of accepting bribes with a value of hundreds of thousands of euros in 2014 and 2015 on behalf of himself and Estonian Centre Party. It was later revealed that Savisaar was also suspected of corruption and money laundering. Because of the ongoing investigation, Savisaar was suspended from mayor's office on 30 September 2015.
Estonian investigative journalist Enno Tammer has theorized that Elmar Savisaar is not Savisaar's biological father, because Elmar Savisaar was arrested already on 8 August 1949. Tammer went on to conclude that if Savisaar was conceived by someone else than his Estonian father, Savisaar may not be entitled to Estonian citizenship.
Edgar Savisaar has been married three times and is the father of four children. From his marriage to Kaire Savisaar he has a son Erki. From his marriage to Liis Remmel (then Liis Savisaar), he has a daughter Maria and son Edgar. The last marriage was to Vilja Toomast (then Vilja Savisaar), who is also an Estonian politician. They had a daughter, Rosina. The couple announced their separation in December 2009.
In March 2015 Savisaar was hospitalized, and due to an infection of Streptococcus bacteria his right leg had to be amputated above the knee.