LionsXII debuted in the 2012 Malaysia Super League on 10 January 2012 with a 1–2 home defeat to defending champions Kelantan FA.

[2] They achieved the biggest win in the season by defeating Sabah FA 9–0 on 16 June 2012.

On 29 December 2012, assistant coach Kadir Yahaya left his position at LionsXII and was replaced by Gombak United FC chief K.

LionsXII began their 2012 Malaysia FA Cup quest on 18 February, with a 3–0 win over UiTM FC.

They eventually bowed out in the semi-finals after losing a penalty shootout to ATM FA with the score tied at 2–2 after extra time.