Presidential elections were held in Indonesia on 5 July 2004, with a second round on 20 September. They were the first direct presidential elections in the country; prior to a 2002 amendment to the Constitution of Indonesia, the President and Vice President had been elected by the People's Consultative Assembly (MPR).

Under the new amendment, a candidate pair is elected into office after receiving more than 50% of the vote nationally with at least 2% of the vote in more than half of the provinces of Indonesia. If no pair receives the number of votes required, the election will continue into the second round with the pairs receiving the highest and second-highest number of votes. Further regulations set by the General Election Commission (KPU) state that each pair must be nominated by a political party or coalition of parties which received at least 5% of the popular vote or 3% of the seats to the People's Representative Council (DPR) in the April legislative election.

The incumbent president, Megawati Sukarnoputri, was sworn into office in 2001 after the legislature impeached and removed her predecessor, president Abdurrahman Wahid (often known as "Gus Dur"), from office. Megawati's re-election bid was challenged by four candidates, including incumbent vice president Hamzah Haz. In the first round, former cabinet member and retired general Susilo Bambang Yudhoyono received a plurality of the valid ballots submitted, followed by Megawati. Yudhoyono eventually defeated Megawati with 60.62% of the valid ballots in the second round. He was inaugurated as the sixth president of Indonesia on 20 October 2004.