On 5 November 2002, he became speaker of the Montenegrin parliament, a position which, from 25 November 2002, made him Acting President of Montenegro due to the resignation of Đukanović from the presidency to prepare to switch office with Vujanović.
Vujanović ran in the December 2002 presidential elections and won a landslide victory, receiving 86% of the vote, but the election was ruled invalid because turnout was less than 50%.
The elections were held again in February 2003, with Vujanović winning 81% of the vote, but again turnout was below 50%.
The elections were held for a third time on 11 May 2003, with the minimum turnout rule abolished, and Vujanović won again with 63% of the vote.

Vujanović resigned from his positions as speaker and acting president on 19 May 2003 but became president of Montenegro again three days later when his term began.
Even though he was born and raised in Serbia, he was one of the most prominent Montenegrin secessionists.
As president of Montenegro, Vujanović was a supporter of the Montenegro independence referendum, though Prime Minister Đukanović was much more high-profile in his campaign for it.
Vujanović's messages often focus on Montenegro's and Serbia's ability to have a peaceful separation and post-independence cooperation, and he is friends with former Serbian president Boris Tadić.
On 21 May 2006, an independence referendum was held in Montenegro; it was approved by 55.5% of voters, narrowly passing the 55% threshold.
On 3 June 2006, Montenegro became an independent state.

On 14 December 2006, he signed the Framework Document for the accession to the Partnership for Peace Programme, wherewith Montenegro became a member of the NATO program "Partnership for Peace".
During the press conference that President Vujanovic and Secretary General of NATO, Jaap de Hoop Scheffer held after signing the Partnership for Peace Framework Document, Scheffer welcomed the way Montenegro decided to go towards the European integrations.

In April 2007, President Vujanović declared he would protect the property of the main religious institution in Montenegro, the Serbian Orthodox Church during an attempt of the non-canonical Montenegrin Orthodox Church to forcibly seize its property.
At the 2008 presidential election, Vujanović ran for the second presidential term, and secured another five years in office in the first election round, with 51.89% vote.
The turnout was 68.2%.

On 20 January 2012, Vujanović adopted the Decision on Calling Elections for the MPs of the local Parliament of Tivat and local Parliament of Herceg Novi.
On 28 March 2012, Vujanović, after carrying out consultations with the Bar Association of Montenegro, Association of Judges of Montenegro, Law faculties, Academy of Sciences, Extended Session of the Supreme Court of Montenegro, appointed four members of the Judicial Council, that were judges of the Constitutional Court of Montenegro.

On July 31, 2012, President Vujanović passed a Decision on Calling Elections for Members of the Parliament of Montenegro.
The parliamentary elections were held on October 14 and were won by the Coalition for European Montenegro, dominated by DPS.
Following the elections, on December 4, 2012, Vujanović destined Đukanović as Prime Minister.

In February 2013, the Constitutional Court officially approved Vujanović's candidacy for a new term, noting that for his 2003–2008 term he was elected as President of the Republic of Montenegro as a constituent entity within its state union with Serbia and served as de facto independent head of state only in 2006–2008, meaning that his 2008–2013 term is legally his first term.
At the 2013 presidential election Vujanović won the election for third presidential term, with 51.2% of the vote against the Democratic Front opposition alliance nominee, Miodrag Lekić.
On 5 November 2002, he became speaker of the Montenegrin parliament, a position which, from 25 November 2002, made him Acting President of Montenegro due to the resignation of Đukanović from the presidency to prepare to switch office with Vujanović. Vujanović ran in the December 2002 presidential elections and won a landslide victory, receiving 86% of the vote, but the election was ruled invalid because turnout was less than 50%. The elections were held again in February 2003, with Vujanović winning 81% of the vote, but again turnout was below 50%. The elections were held for a third time on 11 May 2003, with the minimum turnout rule abolished, and Vujanović won again with 63% of the vote.
Vujanović resigned from his positions as speaker and acting president on 19 May 2003 but became president of Montenegro again three days later when his term began. Even though he was born and raised in Serbia, he was one of the most prominent Montenegrin secessionists. As president of Montenegro, Vujanović was a supporter of the Montenegro independence referendum, though Prime Minister Đukanović was much more high-profile in his campaign for it. Vujanović's messages often focus on Montenegro's and Serbia's ability to have a peaceful separation and post-independence cooperation, and he is friends with former Serbian president Boris Tadić. On 21 May 2006, an independence referendum was held in Montenegro; it was approved by 55.5% of voters, narrowly passing the 55% threshold. On 3 June 2006, Montenegro became an independent state.
On 14 December 2006, he signed the Framework Document for the accession to the Partnership for Peace Programme, wherewith Montenegro became a member of the NATO program "Partnership for Peace". During the press conference that President Vujanovic and Secretary General of NATO, Jaap de Hoop Scheffer held after signing the Partnership for Peace Framework Document, Scheffer welcomed the way Montenegro decided to go towards the European integrations.
In April 2007, President Vujanović declared he would protect the property of the main religious institution in Montenegro, the Serbian Orthodox Church during an attempt of the non-canonical Montenegrin Orthodox Church to forcibly seize its property. At the 2008 presidential election, Vujanović ran for the second presidential term, and secured another five years in office in the first election round, with 51.89% vote. The turnout was 68.2%.
On 20 January 2012, Vujanović adopted the Decision on Calling Elections for the MPs of the local Parliament of Tivat and local Parliament of Herceg Novi. On 28 March 2012, Vujanović, after carrying out consultations with the Bar Association of Montenegro, Association of Judges of Montenegro, Law faculties, Academy of Sciences, Extended Session of the Supreme Court of Montenegro, appointed four members of the Judicial Council, that were judges of the Constitutional Court of Montenegro.
On July 31, 2012, President Vujanović passed a Decision on Calling Elections for Members of the Parliament of Montenegro. The parliamentary elections were held on October 14 and were won by the Coalition for European Montenegro, dominated by DPS. Following the elections, on December 4, 2012, Vujanović destined Đukanović as Prime Minister.
In February 2013, the Constitutional Court officially approved Vujanović's candidacy for a new term, noting that for his 2003–2008 term he was elected as President of the Republic of Montenegro as a constituent entity within its state union with Serbia and served as de facto independent head of state only in 2006–2008, meaning that his 2008–2013 term is legally his first term. At the 2013 presidential election Vujanović won the election for third presidential term, with 51.2% of the vote against the Democratic Front opposition alliance nominee, Miodrag Lekić.
Filip Vujanović