Kelantan defended the title after defeating Johor Darul Ta'zim 1–0 in the final.

2012 winners Kelantan and runners-up Sime Darby have received byes[1] for this edition and will progress straight into the Round of 16.

[2] The draw for the Piala FA 2013 was held at Wisma FAM on 10 December 2012.

Cambodian club Preah Khan Reach is invited for the 2nd time.

The Singapore club LionsXII is also participating for the second time in this competition, after being knocked out in the first round by PKNS to a 1-0 aggregate loss.