FAM later decided to withdraw Harimau Muda B from the league and register them in the 2013 S.League, replacing Harimau Muda A who pulled out of the S.League to embark on a tour of friendly matches in Europe, and preparing them for the 2013 Southeast Asian Games.

Perlis, who originally were relegated after finishing second bottom in 2012 Liga Premier, were reinstated in the league as a result of the withdrawal.

Kuala Lumpur were relegated from 2012 Liga Super after finishing the season in the last place of the 14-team league table.

2012 Malaysia FAM League champions SPA secured direct promotion to this season Liga Premier.

Meanwhile UiTM, the 3rd-place team in FAM League, were invited to replace USM FC, who were withdrawing from Liga Premier due to financial difficulties.