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 Malaysian 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 Takzim F.C. in 2013. In 1994 and 1995, the club won 2 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, Johor FC was promoted to the second tier Malaysian football league, the Malaysian 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 Malaysian 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 Malaysian 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. JDT is the first Malaysian team in the league to have been sponsored by Nike and the first in the country to have its stadium installed with an electronic scoreboard and LED standboard.
JDT started off their season with a disappointing 3–2 lost against Pahang FA despite 2-0 advantage in the first half. On 11 January, JDT registered their first win with Aidil Zafuan scored with a headed goal over a nine-man Perak FA with score of 1-0 at the Larkin Stadium, Johor Bahru.Daniel Güiza scored a 30 metre freekick equaliser against Kelantan FA in a 1–1 draw at Sultan Mohammad IV Stadium, Kota Bharu. On 27 January, JDT announced they are to have a five tier friendly match during a 3 week break of Super League campaign. JDT won 3–0 in their first friendly over Singapore S-League club side Hougang. Daniel Güiza blasted 5 goals in their second friendly against H20 Dream Team in Singapore. JDT beat Geylang United 1–0 before registering a 3–0 win over Singapore Armed Forces. In the last leg of their friendly match, Norshahrul Idlan Talaha helped the team to secure a 1–1 draw with Young Lions. JDT resumed their campaign with a 1-0 victory over T-Team FC to continue their six-match unbeaten run in all competitions, including Super League and FA Cup matches. On 9 March, JDT suffered their second lost of the season to Selangor FA with the final score 4-1. With this, JDT's 10 unbeaten streak has ended. This was their second away-game lost of the season. JDT took the top spot of the Super League on 19 April with a win over Pahang FA at their homeground. This was also Leonel Núñez first goal in the league and third goal in overall competition, since the departure of Daniel Güiza. The Southern Tigers squad suffered 2 consecutive losses to Perak FA and ATM FA, consequently at their away games and thus stacks up to 4 away games loss. JDT managed to bounce back with 4 matches winning streak but with a mixed run of results, saw JDT slipped past some chances to gain back to the top spot. JDT ended their season in 3rd placing behind Selangor FA and Super League champion, LionsXII. To conclude, JDT missed the chance to qualify for the AFC Cup next year.