Following the fall of President Suharto and the end of Indonesia's authoritarian New Order, as a result of public pressure, President Habibie brought forward the general elections planned for 2002 to 1999. On 1 February the People's Representative Council passed Law No. 3/1999 on the General Election, which mandated the establishment of a "free and independent General Elections Commission comprising members of political parties and the government" to oversee the elections. The commission was then established with 53 members and former home affairs minister Rudini as chair. As a result of further public pressure, the government appointed five independent people as its representatives, including noted human rights lawyer Adnan Buyung Nasution. Other independent members included former Supreme Court judge Adi Andojo Soetjipto and political commentator Andi Mallarangeng. The 1999 elections were held on 7 June, and were a success thanks to the management of the KPU, although 27 of the 48 parties contesting the election (all but one of which won less than 0.7% of the vote) refused to sign the KPU document reporting the results. The KPU passed the problem on to President Habibie, who declared the results valid on 26 July.^[1][2][3][4]

The second incarnation of the KPU was established on 11 April 2001 to organise the 2004 elections. This time, however, the People's Representative Council (DPR) passed Law No. 4/2000, which stipulated that the KPU members be made up of nonpartisan individuals from academia and NGOs. In 2007, the People's Representative Council (DPR) passed Law No. 22/2007, which stipulated that members of the KPU serve a five-year term. It also stated that members of the KPU would be chosen by a selection committee that together with the president would put forward a list of names to the DPR, which would conduct a fit and proper test. As a result of this process, which lasted from 21 to 30 August 2007, the initial 45 candidates were whittled down to 21, and a vote was taken by the DPR to decide on the final membership. The seven people chosen for the 2007–2012 term KPU were members of regional KPUs, academics, researchers, and bureaucrats.

KPU central headquarters is located in a building on Jalan Imam Bonjol 29, Central Jakarta. The building, designed by architect A.W. Gmelig Meyling, was completed in 1955 and was among the first to be built in the post-war architecture style in Indonesia. It was described as "impressive" at its completion. The building was originally used for the office of the National Horticulture Centre of the Ministry of Agriculture.^[5]

KPU also has its local offices in all provinces, cities, and regencies throughout Indonesia except Aceh, where it took a name Independent Elections Commission (Komisi Independen Pemilihan or KIP) with its own structure and regulation.

On 12 April 2022, President Joko Widodo, inaugurated members of KPU and Bawaslu for a term of 2022–2027. These are the current members (commissioners) of KPU:

• General Election Supervisory Agency
• Elections in Indonesia

• Abdullah, Taufik (April 2009). Indonesia: Towards Democracy. Solo: Institute of Southeast Asian Studies. ISBN 978-981-2303660.
• Manning, Chris; van Dierman, Peter (April 2000). Indonesia in Transition: Social Aspects of Reformasi and Crisis. Institute of Southeast Asian Studies. ISBN 978-1856499248.
• Merrillees, Scott (2015). Jakarta: Portraits of a Capital 1950-1980. Jakarta: Equinox Publishing. ISBN 9786028397308.
• Puspoyo, Widjanarko (December 2012). Dari Soekarno Hingga Yudhoyono, Pemilu Indonesia 1955 - 2009 (From Soekarno to Yudhoyono. Indonesian General Elections 1955 - 2009). Solo: Eka Adicitra Intermedia. ISBN 9786028237970.
• "Profil Komisi Pemilihan Umum (Profile of the General Elections Commission)" (in Indonesian). KPU. Retrieved 25 March 2014.