It started on 1 September 2012 and ended on 1 January 2013 with the final at National Stadium in Tokyo, Japan, won by Kashiwa Reysol 1–0 against Gamba Osaka.
The cup winners were guaranteed a place in the 2013 AFC Champions League.
(*1) The team was the prefectural runners-up; Both Nagasaki Prefectural Cup finalists qualified for the final tournament, after the other finalist, V-Varen Nagasaki, had qualified to the Emperor's Cup as the JFL seeded club.
[1] Since this year, the drawing of the tournament will be held twice: The first draw determine the pairings of first to third round matches; the second draw will be held after the third round that determines the pairings of the fourth round to the final.
Note: The venue was changed on 21 September, originally planned to be Hiroshima Big Arch Main Stadium.