The second round is played from 28 Juny 2013 to 30 August 2013. notes : 1 Mojokerto Putra loses 3–0 against Perseru Serui after did not attend the match on 24 August 2013 in Marora Stadium.
Babak kedua ini dilaksanakan mulai tanggal 28 Juni 2013 hingga 30 Agustus 2013. notes : 1 Mojokerto Putra loses 3−0 against Perseru Serui after did not attend the match on 24 August 2013 in Marora Stadium.