JDT II was founded as Johor FA in 1955 and are known as one of the "second-wave" football teams to participated in Malaysian football league (first-wave are Kedah, Selangor etc.;). In its early years, the team was based in Kluang, Johor under the guidance of its Johor Football Association. In 1964, the southern-side team moved to Tan Sri Dato' Haji Hassan Yunos Stadium. Few changes in the management of Johor Football Association in the 1970s saw Datuk Suleiman Mohd Noor appointed as president and team manager. Under his management, the team rose as a formidable team in the football scene. This was proven some years later when JDT II won Piala Razak trophy in 1983 and their first ever Malaysia Cup trophy in 1985 and also Piala Sultan Haji Ahmad Shah (better known as Piala Sumbangsih) in 1986 under then coach, Ahmad Esa. When the game went Semi-Pro in 1989, Johor are the first team that won the Malaysia Cup and the Malaysia League in 1991, thus achieved a "Grand Double", first ever by a team in this country during that Semi-Pro period. It was also a second Malaysia Cup for the Johor team. In 1992, JDT II finished seventh in the league, their worst standings since 1989. This was proven crucial for the former coach, Michael Urukalo, as he was dismissed and replaced by Wan Jamak Wan Hassan. JDT II see off their 1993 season well, standing at fifth position even without two of their cup-winners import players, Abbas Saad and Alistair Edwards. The team then went on with years of trophyless drought until 1998, when they won their first FA Cup. Next season saw that the team clinched promotion to top division in winning the Malaysia Premier League title. JDT II had a tough seasons in the Premier One League and finally were relegated back to Premier Two League in 2001 after two years in top-flight division. For the 2006–07 Malaysia Premier League competition, Johor FA decided to compete under the sponsored name Johor PBT Pasir Gudang (or Johor Pasir Gudang). They were given the green light by Football Association of Malaysia on 9 January 2007 to compete under the new name. Reasons behind the change for the team's name are controversial because the team had to merged with now-defunct Pasir Gudang United F.C. which caused an unrest amongst supporters. However, there are another reason because the Pasir Gudang Local Authority (PBTPG), now known as Majlis Perbandaran Pasir Gudang (MPPG), is Johor FA's main sponsor during that season.