| 1 | |  Oita Trinata | 30 | 19 | 4 | 7 | 50 | 24 | 26 | 61 | G07:00 | 20/11/16 | R 30  Gainare Tottori 2 Oita Trinata 4 G07:00 | 13/11/16 | R 29 Oita Trinata 3 YSCC Yokohama 0 G07:00 | 06/11/16 | R 28 Oita Trinata 1 Gamba Osaka U23 0 G07:00 | 30/10/16 | R 27 Blaublitz Akita 0 Oita Trinata 1 G08:00 | 23/10/16 | R 26 Oita Trinata 4 Iwate Grulla Morioka 2 M07:00 | 16/10/16 | R 25 AC Nagano Parceiro 1 Oita Trinata 0 |
| 2 | |  Tochigi SC | 30 | 17 | 8 | 5 | 38 | 20 | 18 | 59 | B07:00 | 20/11/16 | R 30 Iwate Grulla Morioka 2 Tochigi SC 2 M07:00 | 13/11/16 | R 29 Tochigi SC 0 AC Nagano Parceiro 1 G07:00 | 05/11/16 | R 28 Gainare Tottori 0 Tochigi SC 1 G07:00 | 30/10/16 | R 27 Tochigi SC 2 Kataller Toyama 0 B07:00 | 23/10/16 | R 26 Fujieda MYFC 1 Tochigi SC 1 G07:00 | 16/10/16 | R 25 Tochigi SC 3 Fukushima United FC 1 |
| 3 | |  AC Nagano Parceiro | 30 | 15 | 7 | 8 | 33 | 22 | 11 | 52 | G07:00 | 20/11/16 | R 30 AC Nagano Parceiro 1 Kagoshima United 0 G07:00 | 13/11/16 | R 29 Tochigi SC 0 AC Nagano Parceiro 1 G07:00 | 05/11/16 | R 28 FC Tokyo U23 1 AC Nagano Parceiro 2 B07:00 | 30/10/16 | R 27 AC Nagano Parceiro 0 Iwate Grulla Morioka 0 M10:00 | 23/10/16 | R 26 FC Ryukyu 2 AC Nagano Parceiro 1 G07:00 | 16/10/16 | R 25 AC Nagano Parceiro 1 Oita Trinata 0 |
| 4 | |  Blaublitz Akita | 30 | 14 | 8 | 8 | 37 | 26 | 11 | 50 | G07:00 | 20/11/16 | R 30 Blaublitz Akita 2 FC Ryukyu 0 B08:00 | 13/11/16 | R 29 Gamba Osaka U23 2 Blaublitz Akita 2 G07:00 | 06/11/16 | R 28 Blaublitz Akita 2 SC Sagamihara 1 M07:00 | 30/10/16 | R 27 Blaublitz Akita 0 Oita Trinata 1 G08:00 | 22/10/16 | R 26 Cerezo Osaka U23 1 Blaublitz Akita 2 M07:00 | 16/10/16 | R 25 Kagoshima United 1 Blaublitz Akita 0 |
| 5 | |  Kagoshima United | 30 | 15 | 5 | 10 | 39 | 29 | 10 | 50 | M07:00 | 20/11/16 | R 30 AC Nagano Parceiro 1 Kagoshima United 0 B07:10 | 13/11/16 | R 29 Kagoshima United 2 Iwate Grulla Morioka 2 M07:00 | 06/11/16 | R 28 Fujieda MYFC 2 Kagoshima United 0 M07:00 | 30/10/16 | R 27 Kagoshima United 1 FC Ryukyu 2 G07:00 | 23/10/16 | R 26 SC Sagamihara 0 Kagoshima United 4 G07:00 | 16/10/16 | R 25 Kagoshima United 1 Blaublitz Akita 0 |
| 6 | |  Kataller Toyama | 30 | 13 | 10 | 7 | 37 | 29 | 8 | 49 | B07:00 | 20/11/16 | R 30 Kataller Toyama 1 SC Sagamihara 1 G08:00 | 13/11/16 | R 29 Cerezo Osaka U23 2 Kataller Toyama 3 B07:00 | 06/11/16 | R 28 Kataller Toyama 1 FC Ryukyu 1 M07:00 | 30/10/16 | R 27 Tochigi SC 2 Kataller Toyama 0 G07:00 | 23/10/16 | R 26 Gainare Tottori 0 Kataller Toyama 1 B07:00 | 16/10/16 | R 25 Kataller Toyama 0 FC Tokyo U23 0 |
| 7 | |  Fujieda MYFC | 30 | 14 | 3 | 13 | 48 | 42 | 6 | 45 | G07:00 | 20/11/16 | R 30 Fujieda MYFC 2 Fukushima United FC 0 M07:00 | 13/11/16 | R 29 SC Sagamihara 3 Fujieda MYFC 1 G07:00 | 06/11/16 | R 28 Fujieda MYFC 2 Kagoshima United 0 G08:00 | 30/10/16 | R 27 YSCC Yokohama 0 Fujieda MYFC 3 B07:00 | 23/10/16 | R 26 Fujieda MYFC 1 Tochigi SC 1 G07:00 | 16/10/16 | R 25 Fujieda MYFC 4 Gamba Osaka U23 0 |
| 8 | |  FC Ryukyu | 30 | 12 | 8 | 10 | 46 | 46 | 0 | 44 | M07:00 | 20/11/16 | R 30 Blaublitz Akita 2 FC Ryukyu 0 B09:00 | 13/11/16 | R 29 FC Ryukyu 1 Gainare Tottori 1 B07:00 | 06/11/16 | R 28 Kataller Toyama 1 FC Ryukyu 1 G07:00 | 30/10/16 | R 27 Kagoshima United 1 FC Ryukyu 2 G10:00 | 23/10/16 | R 26 FC Ryukyu 2 AC Nagano Parceiro 1 G07:00 | 16/10/16 | R 25 YSCC Yokohama 0 FC Ryukyu 2 |
| 9 | |  Gamba Osaka U23 | 30 | 10 | 8 | 12 | 42 | 41 | 1 | 38 | M07:00 | 20/11/16 | R 30 YSCC Yokohama 2 Gamba Osaka U23 0 B08:00 | 13/11/16 | R 29 Gamba Osaka U23 2 Blaublitz Akita 2 M07:00 | 06/11/16 | R 28 Oita Trinata 1 Gamba Osaka U23 0 M08:00 | 30/10/16 | R 27 Gamba Osaka U23 1 Gainare Tottori 2 B08:00 | 23/10/16 | R 26 Gamba Osaka U23 1 FC Tokyo U23 1 M07:00 | 16/10/16 | R 25 Fujieda MYFC 4 Gamba Osaka U23 0 |
| 10 | |  FC Tokyo U23 | 30 | 9 | 9 | 12 | 32 | 31 | 1 | 36 | G07:00 | 20/11/16 | R 30 FC Tokyo U23 2 Cerezo Osaka U23 0 G07:00 | 13/11/16 | R 29 Fukushima United FC 0 FC Tokyo U23 2 M07:00 | 05/11/16 | R 28 FC Tokyo U23 1 AC Nagano Parceiro 2 G08:00 | 30/10/16 | R 27 FC Tokyo U23 4 SC Sagamihara 1 B08:00 | 23/10/16 | R 26 Gamba Osaka U23 1 FC Tokyo U23 1 B07:00 | 16/10/16 | R 25 Kataller Toyama 0 FC Tokyo U23 0 |
| 11 | |  SC Sagamihara | 30 | 9 | 8 | 13 | 29 | 46 | -17 | 35 | B07:00 | 20/11/16 | R 30 Kataller Toyama 1 SC Sagamihara 1 G07:00 | 13/11/16 | R 29 SC Sagamihara 3 Fujieda MYFC 1 M07:00 | 06/11/16 | R 28 Blaublitz Akita 2 SC Sagamihara 1 M08:00 | 30/10/16 | R 27 FC Tokyo U23 4 SC Sagamihara 1 M07:00 | 23/10/16 | R 26 SC Sagamihara 0 Kagoshima United 4 M07:00 | 16/10/16 | R 25 Iwate Grulla Morioka 5 SC Sagamihara 0 |
| 12 | |  Cerezo Osaka U23 | 30 | 8 | 8 | 14 | 38 | 47 | -9 | 32 | M07:00 | 20/11/16 | R 30 FC Tokyo U23 2 Cerezo Osaka U23 0 M08:00 | 13/11/16 | R 29 Cerezo Osaka U23 2 Kataller Toyama 3 B07:00 | 06/11/16 | R 28 YSCC Yokohama 2 Cerezo Osaka U23 2 B08:00 | 29/10/16 | R 27 Cerezo Osaka U23 2 Fukushima United FC 2 M08:00 | 22/10/16 | R 26 Cerezo Osaka U23 1 Blaublitz Akita 2 G07:00 | 16/10/16 | R 25 Gainare Tottori 1 Cerezo Osaka U23 2 |
| 13 | |  Iwate Grulla Morioka | 30 | 6 | 12 | 12 | 43 | 47 | -4 | 30 | B07:00 | 20/11/16 | R 30 Iwate Grulla Morioka 2 Tochigi SC 2 B07:10 | 13/11/16 | R 29 Kagoshima United 2 Iwate Grulla Morioka 2 G07:00 | 05/11/16 | R 28 Iwate Grulla Morioka 4 Fukushima United FC 2 B07:00 | 30/10/16 | R 27 AC Nagano Parceiro 0 Iwate Grulla Morioka 0 M08:00 | 23/10/16 | R 26 Oita Trinata 4 Iwate Grulla Morioka 2 G07:00 | 16/10/16 | R 25 Iwate Grulla Morioka 5 SC Sagamihara 0 |
| 14 | |  Fukushima United FC | 30 | 7 | 9 | 14 | 35 | 44 | -9 | 30 | M07:00 | 20/11/16 | R 30 Fujieda MYFC 2 Fukushima United FC 0 M07:00 | 13/11/16 | R 29 Fukushima United FC 0 FC Tokyo U23 2 M07:00 | 05/11/16 | R 28 Iwate Grulla Morioka 4 Fukushima United FC 2 B08:00 | 29/10/16 | R 27 Cerezo Osaka U23 2 Fukushima United FC 2 G07:00 | 23/10/16 | R 26 Fukushima United FC 2 YSCC Yokohama 0 M07:00 | 16/10/16 | R 25 Tochigi SC 3 Fukushima United FC 1 |
| 15 | |  Gainare Tottori | 30 | 8 | 6 | 16 | 30 | 47 | -17 | 30 | M07:00 | 20/11/16 | R 30 Gainare Tottori 2 Oita Trinata 4 B09:00 | 13/11/16 | R 29 FC Ryukyu 1 Gainare Tottori 1 M07:00 | 05/11/16 | R 28 Gainare Tottori 0 Tochigi SC 1 G08:00 | 30/10/16 | R 27 Gamba Osaka U23 1 Gainare Tottori 2 M07:00 | 23/10/16 | R 26 Gainare Tottori 0 Kataller Toyama 1 M07:00 | 16/10/16 | R 25 Gainare Tottori 1 Cerezo Osaka U23 2 |
| 16 | |  YSCC Yokohama | 30 | 5 | 5 | 20 | 15 | 51 | -36 | 20 | G07:00 | 20/11/16 | R 30 YSCC Yokohama 2 Gamba Osaka U23 0 M07:00 | 13/11/16 | R 29 Oita Trinata 3 YSCC Yokohama 0 B07:00 | 06/11/16 | R 28 YSCC Yokohama 2 Cerezo Osaka U23 2 M08:00 | 30/10/16 | R 27 YSCC Yokohama 0 Fujieda MYFC 3 M07:00 | 23/10/16 | R 26 Fukushima United FC 2 YSCC Yokohama 0 M07:00 | 16/10/16 | R 25 YSCC Yokohama 0 FC Ryukyu 2 |
