Schedule
| Round | Date | Fixture | Clubs | Byes/Exemptions |
|---|---|---|---|---|
| First Round | September 17 and 18 | 20 | 40→20 | 39: non-seeded prefectural representative clubs 1: University representative |
| Second Round | September 23 and 24 | 14 | 20+8→14 | 8: seeded prefectural representative clubs |
| Third Round | October 8 | 14 | 14+13+1→14 | 14: J2 clubs (13) and JFL Champions |
| Fourth Round | November 4, 5 and 8 | 16 | 14+18→16 | 18: J1 clubs |
| Fifth Round | December 9 and 16 | 8 | 16→8 | |
| Quarterfinals | December 23 | 4 | 8→4 | |
| Semifinals | December 29 | 2 | 4→2 | |
| Final | January 1, 2007 | 1 | 2→1 |
Read more about this topic: 2006 Emperor's Cup