Contested against Congress candidate and former MP Pratap Bhanu Sharma from Vidisha, Chouhan won the Lok Sabha election by a huge margin of 8,21,408 votes.

After his stint with the Akhil Bharatiya Vidyarthi Parishad (ABVP), the student wing of the RSS, during his college days in Bhopal, Chauhan made his electoral debut in 1990, when he won the assembly elections from his hometown Budhni in Sehore district.

A year later, Chouhan contested the by-election after the Vidisha Lok Sabha seat was vacated by former Prime Minister late Atal Bihari Vajpayee and defeated Congress's Pratap Bhanu Sharma by over 1 lakh votes.

He retained this seat for four consecutive terms from 1996 to 2004.

Making a comeback in the state elections, Chauhan won the assembly elections from Budhni in 2006, 2008, 2013, 2018 and 2023.In 2003, when the BJP ousted the Digvijay Singh-led Congress government in Madhya Pradesh, Uma Bharti was made the Chief Minister. In August 2004, he was replaced by veteran BJP leader Babulal Gaur.

A year later, Chouhan replaced Gaur as chief minister and remained in the chair until 2018 as the BJP won two assembly elections under his leadership – 2008 and 2013 – before losing to the Congress in 2018.

However, the Congress government did not last long as a faction led by Jyotiraditya Scindia and 22 of his loyal MLAs defected to the BJP in March 2020, paving the way for Chouhan's return as CM for a fourth term.

The BJP won the assembly elections in 2023 despite being in power, but on December 3, Chouhan was replaced by Mohan Yadav as the new chief minister.During his tenure of over 17 years as Chief Minister, Chouhan launched several public beneficiary schemes in Madhya Pradesh, including the 'Laadli Laxmi Yojana' in 2008, which earned him the sobriquet 'Mama'.

In 2023, he extended his popular scheme with a new name 'Laadli Behna Yojana', a provision of cash benefits for women on 163 out of 230 seats in the assembly elections.