Johor FC was founded in 1972 under the Sports Bureau of the Workers Union of Johor State Economic Development Corporation (Perbadanan Kemajuan Ekonomi Negeri Johor). Thus the team was then named Perbadanan Kemajuan Ekonomi Negeri Johor FC (PKENJ FC). The team started joining the local Johor Bahru Football Association League since its foundation and was the regular winner of the league. In 1988, the team qualified for the FAM Cup. In 1994 and 1995, Johor FC won 2 consecutive FAM Cups, and was the runner-up in 1996. From 1997 to 2001, Johor FC played in the second-tier football league in Malaysia, the Malaysia Premier League (which was then known as the Premier-Two League), and was the champion for the season 2001.
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