In 1990, Rahmon was elected a people's deputy to the Supreme Soviet of the Tajik SSR.
President Rahmon Nabiyev was forced to resign in the first months of the Civil War in Tajikistan in August 1992.
Akbarsho Iskandarov, Speaker of the Supreme Soviet, became acting president.
Iskandarov resigned in November 1992 in an attempt to end the civil unrest.
That same month, the Supreme Soviet met in Khujand for its 16th session and declared Tajikistan a parliamentary republic.
Rahmon was then elected by the members of the Supreme Soviet as its chairman—a post equivalent to that of president—and the head of government.

During the civil war that lasted from 1992–97, Rahmon's rule was opposed by the United Tajik Opposition.
As many as 100,000 people died during the war.
He survived an assassination attempt on 30 April 1997 in Khujand, as well as two attempted coups in August 1997 and in November 1998.

In 1994, a new constitution reestablished the presidency.
 Rahmon was elected to the post on 6 November 1994 and sworn in ten days later.
Following constitutional changes, he was reelected on 6 November 1999 to a seven-year term, officially taking 97% of the vote.
On 22 June 2003, he won a referendum that would allow him to run for two more consecutive seven-year terms after his term expired in 2006.
The opposition alleges that this amendment was hidden in a way that verged upon electoral fraud.
Rahmon was reelected to a seven-year term in a controversial election on 6 November 2006, with about 79% of the vote, according to the official results.
On 6 November 2013, he was reelected for the second seven-year term in office, with about 84% of the vote, in an election that the Organization for Security and Co-operation in Europe said lacked "genuine choice and meaningful pluralism".

In December 2015, a law passed by Tajikistan's parliament gave Rahmon the title "Founder Of Peace and National Unity, Leader of the Nation" (Tajik: Асосгузори сулҳу ваҳдати миллӣ – Пешвои миллат, Asosguzori sulhu vahdati millî – Peşvo‘i millat; Russian: Основатель мира и национального единства – Лидер нации, Osnovatel mira i natsionalnogo yedinstva – Lider natsii).
A shorter version of the title, "Leader of the Nation," is used frequently.
In addition to granting Rahmon lifelong immunity from prosecution, the law also gave him a number of other lifelong privileges, including veto powers over all major state decisions, the freedom to address the nation and parliament on all matters he deems important, and the privilege of attending all government meetings and parliament sessions.

On 22 May 2016, a nationwide referendum approved a number of changes to the country's constitution.
One of the main changes lifted the limit on presidential terms, effectively allowing Rahmon to stay in power for as many terms as he wishes.
Other key changes outlawed faith-based political parties, thus finalizing the removal of the outlawed Islamic Revival Party from Tajikistan's politics, and reduced the minimum eligibility age for presidential candidates from 35 to 30, enabling Rahmon's older son, Rustam Emomali, to run for president any time after 2017.
In January 2017, Rustam Emomali was appointed Mayor of Dushanbe, a key position, which some analysts see as the next step to the top of the government.

According to the US ambassador in Tajikistan, Rahmon's government is characterized by cronyism and corruption.
Rahmon and his family control the country's major businesses, including the largest bank.
In November 2018, Rahmon launched a hydroelectric station to solve energy problems.
In 1990, Rahmon was elected a people's deputy to the Supreme Soviet of the Tajik SSR. President Rahmon Nabiyev was forced to resign in the first months of the Civil War in Tajikistan in August 1992. Akbarsho Iskandarov, Speaker of the Supreme Soviet, became acting president. Iskandarov resigned in November 1992 in an attempt to end the civil unrest. That same month, the Supreme Soviet met in Khujand for its 16th session and declared Tajikistan a parliamentary republic. Rahmon was then elected by the members of the Supreme Soviet as its chairman—a post equivalent to that of president—and the head of government.
During the civil war that lasted from 1992–97, Rahmon's rule was opposed by the United Tajik Opposition. As many as 100,000 people died during the war. He survived an assassination attempt on 30 April 1997 in Khujand, as well as two attempted coups in August 1997 and in November 1998.
In 1994, a new constitution reestablished the presidency.  Rahmon was elected to the post on 6 November 1994 and sworn in ten days later. Following constitutional changes, he was reelected on 6 November 1999 to a seven-year term, officially taking 97% of the vote. On 22 June 2003, he won a referendum that would allow him to run for two more consecutive seven-year terms after his term expired in 2006. The opposition alleges that this amendment was hidden in a way that verged upon electoral fraud. Rahmon was reelected to a seven-year term in a controversial election on 6 November 2006, with about 79% of the vote, according to the official results. On 6 November 2013, he was reelected for the second seven-year term in office, with about 84% of the vote, in an election that the Organization for Security and Co-operation in Europe said lacked "genuine choice and meaningful pluralism".
In December 2015, a law passed by Tajikistan's parliament gave Rahmon the title "Founder Of Peace and National Unity, Leader of the Nation" (Tajik: Асосгузори сулҳу ваҳдати миллӣ – Пешвои миллат, Asosguzori sulhu vahdati millî – Peşvo‘i millat; Russian: Основатель мира и национального единства – Лидер нации, Osnovatel mira i natsionalnogo yedinstva – Lider natsii). A shorter version of the title, "Leader of the Nation," is used frequently. In addition to granting Rahmon lifelong immunity from prosecution, the law also gave him a number of other lifelong privileges, including veto powers over all major state decisions, the freedom to address the nation and parliament on all matters he deems important, and the privilege of attending all government meetings and parliament sessions.
On 22 May 2016, a nationwide referendum approved a number of changes to the country's constitution. One of the main changes lifted the limit on presidential terms, effectively allowing Rahmon to stay in power for as many terms as he wishes. Other key changes outlawed faith-based political parties, thus finalizing the removal of the outlawed Islamic Revival Party from Tajikistan's politics, and reduced the minimum eligibility age for presidential candidates from 35 to 30, enabling Rahmon's older son, Rustam Emomali, to run for president any time after 2017. In January 2017, Rustam Emomali was appointed Mayor of Dushanbe, a key position, which some analysts see as the next step to the top of the government.
According to the US ambassador in Tajikistan, Rahmon's government is characterized by cronyism and corruption. Rahmon and his family control the country's major businesses, including the largest bank. In November 2018, Rahmon launched a hydroelectric station to solve energy problems.
Emomali Rahmon