The 2016 season was Negeri Sembilan's 93th year in their history and 5th season in Malaysia Premier League since it was first introduced in 2004. Also it was the third season in the Malaysia Premier League following relegation on 2013 season. Along with the league, the club also participated in the Malaysia FA Cup and the Malaysia Cup.
Negeri Sembilan has changed the name of the team from Negeri Sembilan Matrix to Negeri Sembilan FA for the 2016 season. This decision was made in 2015 when the president of Negeri Sembilan was not satisfied with the performance of the team throughout the 2015 season until it failed to qualify for the Malaysia Cup and considered the NS Matrix project a failure. The team was restructured with the inclusion of young players and the dismissal of head coach K. Devan.
On 24 November 2015, Gary Phillips was appointed as the new head coach for the Negeri Sembilan team. This head coach is an experienced coach in the Malaysian football league and was the head coach for the Sabah team from 2009 to 2011. He was appointed to replace K. Devan, who had previously coached the team for the 2015 season.
On 20 May 2016, in the 12th match of the Premier League, Negeri Sembilan defeated the UiTM team by a score of 4-2, which made the Negeri Sembilan team top of the league, but were overtaken by the Melaka United team the next day when they defeated ATM, 4-2. From the 6th week to the 12th week showing, the teams of Negeri Sembilan, Kuala Lumpur and Melaka United competed to be in the top of the league.
On 17 September 2016, Negeri Sembilan was eliminated from the Malaysia Cup when they lost 0âÂÂ5 to the Kedah FA at the Darul Aman Stadium. In the first leg, Negeri Sembilan only drew at home after each failed to score a goal in a 0âÂÂ0 result. The advantage of 1 point in the opponent's place was used well by Kedah when they managed to bury Negeri Sembilan in the second leg without any pressure. Negeri Sembilan has stopped the 2016 Malaysia Cup campaign by only making it to the quarter-finals.
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In the competition, the top 11 teams from the First Round of 2016 Malaysia Super League were joined by the top 5 teams from the First Round of 2016 Malaysia Premier League. The teams were drawn into four groups of four teams.
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The first legs were played on 28 August 2016, and the second legs were played on 17 September 2016.
First Leg
Second Leg