Match were held during mid-season break and matches were held between 25 March and 4 July 2016. Several foreign players made a trial with the team for second window transfer.
^Since the winners of 2016 Piala FA, Johor Darul Ta'zim, currently qualify for AFC Champions League based on their league position, the spot awarded to the Piala FA winner (AFC Cup group stage) would be passed to the next best team in the table (in this case, the second-placed team).
^Kedah Football Association (Kedah FA) has been found guilty of putting the suspended player during the match against Pahang on August 3, 2016. Therefore, the Football Association of Malaysia (FAM) has been awarded 3 points for Pahang and Kedah sentenced deducted 3 points for the incident.
PC is a Presiden Cup player who have played for the senior team as a starter, substitute or benched
Playing statistics
Key:
= Appearances,
= Goals,
= Yellow card,
= Red card Player names in bold denotes player that left mid-season (loaned) (number in bracket denotes the players plays as a substitute in a match)