After the demise of his father Biju Patnaik, leader of the Janata Dal, Naveen Patnaik contested Lok Sabha by-polls from Aska Parliamentary Constituency in Odisha. He was a member of the Consultative Committee of Ministry of Steel & Mines, Member of Standing Committee on Commerce, and Member Library Committee of Parliament in the 11th Lok Sabha. A year later, the Janata Dal split and he founded the Biju Janata Dal (BJD) on his father’s name. BJD later in alliance with the BJP-led National Democratic Alliance (NDA) performed well in electoral poll and Patnaik became the Union Minister for Mines in the cabinet of Late Atal Bihari Vajpayee.
In 2000 Assembly election, BJD won the majority of seats in alliance with the BJP in the Odisha Assembly elections. Naveen resigned from the Union cabinet portfolio and unanimously elected as the leader of the alliance and was sworn in as the Chief Minister of Odisha.
BJP led NDA lost the general elections in 2004, however the coalition led by Naveen Patnaik emerged victorious in the state legislative elections and he continued as the Chief Minister. During this tenure, the differences between the ruling partners became more and more apparent which led to parting ways.
In the run-up to the polls for the Lok Sabha and Legislative Assembly of Odisha elections in 2009, BJD walked out of the NDA after severing ties with the BJP and joined the nascent Third-Front constituted mainly by the Left Front and few regional parties. He did it after severely criticising BJP's involvement in Kandhamal anti-Christian riots during 2007. The BJD won a resounding victory in both the Vidhan Sabha (State Assembly) as well as the Lok Sabha elections in 2009, winning 14 out of 21 Lok Sabha seats and 103 of the 147 assembly seats and was sworn in as the Chief Minister of Odisha on 21 May 2009 for the third consecutive term.
Patnaik won a huge victory in both the 2014 Indian General Elections and the Legislative Assembly of Odisha elections in 2014. Patnaik's Biju Janata Dal secured 20 out of the 21 Lok Sabha seats of Odisha and 117 of the 147 Odisha Vidhan Sabha seats.
Despite a strong BJP wave across the country, the Biju Janata Dal, under the leadership of Naveen Patnaik won as many as 112 seats out of 146 (polls for 1 was deferred) in the Legislative Assembly of Odisha and 12 out of 21 Lok Sabha seats in 2019 Indian General Election.