The club was formed as
Pelita Jaya Football Club in 1986, based in
Jakarta. During that time, the team won three
Galatama titles (1988–89, 1990, and 1993–94). Starting from 2000, the team moved home grounds several times, first to
Solo in 2000,
Cilegon in 2002,
Purwakarta in 2006,
Bandung in 2008, and
Karawang in 2009, before moving back to Bandung in 2012 after
Bakrie Group sold off the club in favor of purchasing
Arema, which also cancelled a plan to merge the two clubs. Throughout those years, the team retained the "Pelita" name until it was rebranded as
Persipasi Bandung Raya (PBR, which also the abbreviation for the final iteration of the club under the "Pelita" name,
Pelita Bandung Raya) for the ultimately abandoned
2015 Indonesia Super League; despite the name, Persipasi's home base was actually in
Bekasi. On 10 January 2016, an agreement was reached with the previous owner of Persipasi Bandung Raya, Ari Dewanto Sutedi, and Husodo Angkosubroto, witnessed by the founder of Pelita Jaya, Nirwan Dermawan Bakrie, that the ownership of Persipasi Bandung Raya (PBR) was to be taken over and moved to
Madura. The club was rebranded as
Madura United. After the purchase, Madura United replaced PBR to compete in the
2016 Indonesia Soccer Championship A. In 2024, fresh off their
2023–24 Liga 1 runner-up finish, Madura United participated in the inaugural
2024–25 AFC Challenge League tournament being placed in Group E alongside Cambodian club
Preah Khan Reach Svay Rieng and Mongolian club
SP Falcons where the club played both of their match in
Ulaanbaatar. On 27 October 2024, Madura United faced SP Falcons in a goalless contest at the
MFF Football Centre with both team sharing the points. In the next match, Madura United defeated Preah Khan Reach Svay Rieng 2–1 and advanced to the quarter-finals as the group leaders, facing off against Taiwanese club
Tainan City where Madura United was caught with a goalless draw in the first leg at the
Kaohsiung Nanzih Football Stadium. In the second leg, Madura United went on to win the match 3–0 thus qualifying to the semi-finals. However, their progress had to stop in the semi-final round, after losing 3–6 on aggregate (leg 1: Madura United lost 0–3, away; leg 2: drew 3–3, home) against Preah Khan Reach Svay Rieng. ==Name changes==