During 2012, Johor Football Association adopted the two-teams concept, which is Johor Darul Ta'zim F.C. representing the state of Johor for the Malaysia Super League and Johor Darul Ta'zim II F.C. for Malaysia Premier League, with the second team designed to groom young Johorean players who will be representing the first team in the future.
1972–1996: Perbadanan Kemajuan Ekonomi Negeri Johor Football Club (PKENJ FC)
1996–2012: Johor Football Club (Johor FC)
2012-2013: Darul Takzim FC/Johor Darul Takzim Football Club (Johor Darul Takzim FC)
2013–present: Johor Darul Ta'zim Football Club (Johor Darul Ta'zim FC)
JDT was founded as Kelab Bolasepak Perbadanan Kemajuan Ekonomi Negeri Johor (PKENJ F.C.) and established itself under the guidance of the PKENJ Recreation Bureau. The club participated in state football competitions before it premiered in the Malaysia football league in 1988 in the FAM Cup. The club changed its name to Johor FC in 1996, Darul Takzim F.C. in 2012 and finally to Johor Darul Ta'zim F.C. in 2013. In 1994 and 1995, the club won two consecutive FAM Cup titles as PKENJ FC and was the runner-up in 1996 as Johor FC. JDT holds the record for longest period in M-League (Malaysia League) competition by any football club in Malaysia since 1997.
In 1997, JDT was promoted to the second tier Malaysian football league, the Malaysia Premier League (which was then known as the Premier-Two League), and won the title in 2001. After two years in top division of the league, JDT were relegated to Malaysia Premier League during the 2002–2003 season. The club earned an automatic promotion to the Super League during the 2006–2007 season after FAM's decision to expand the league to 14 teams and was respectively a regular top 6 finisher in the league. The club was the first club team in Malaysian football league to enter Malaysia Cup in 2000 under former British manager, Bruce Stowell. Malaysia Cup was previously dominated by state teams and by defeating ATM FA on aggregate in the second-round group qualification, the club itself has marked another record in the division. The club has also participated in AFC Cup in 2009 replacing Negeri Sembilan FA of which the latter qualified but did not proceed to compete in the competition.
The stadium was built in 1964, but back then it was a minor venue with only some 15,000 people to accommodate. In 1991 capacity doubled after an extensive revamp. Athletics track, floodlight masts and media infrastructure also came allowing the ground to host major events. Johor plays their games at Larkin Stadium.