The 1999 Formula Nippon Championship was contested over 10 rounds, 14 different teams, 26 different drivers, 3 different chassis and only 1 engine competed in the championship.
All races were held in Japan.
| Position | 1st | 2nd | 3rd | 4th | 5th | 6th |
|---|---|---|---|---|---|---|
| Points | 10 | 6 | 4 | 3 | 2 | 1 |
| Rank | Name | SUZ | MOT | MIN | FUJ | SUZ | SGO | FUJ | MIN | MOT | SUZ | Points |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | | 2 | Ret | 3 | 1 | 2 | 1 | 1 | Ret | 3 | Ret | 50 |
| 2 | | 1 | 2 | 1 | Ret | Ret | 2 | 3 | Ret | 1 | Ret | 46 |
| 3 | | 3 | 1 | 8 | 10 | 5 | 11 | 4 | 1 | 5 | 9 | 31 |
| 4 | | Ret | 3 | 2 | 9 | Ret | 6 | 10 | 9 | 8 | 1 | 21 |
| 5 | | 5 | Ret | 3 | 11 | 4 | 9 | 4 | Ret | 2 | 19 | |
| 6 | | Ret | Ret | 6 | 12 | 1 | Ret | Ret | Ret | 4 | 4 | 17 |
| 7 | | 4 | 6 | 5 | 2 | Ret | Ret | 5 | 5 | 10 | 10 | 16 |
| 8 | | Ret | 15 | 10 | Ret | 9 | 5 | 2 | 3 | 11 | 3 | 16 |
| 9 | | Ret | Ret | 12 | 5 | 3 | 3 | 10 | ||||
| 10 | | 6 | 8 | 7 | 8 | Ret | Ret | 7 | Ret | 2 | 5 | 9 |
| 11 | | Ret | 16 | 13 | 14 | 6 | Ret | Ret | 2 | 9 | 11 | 7 |
| 12 | | DNS | DNS | 4 | 4 | 8 | 9 | 8 | Ret | Ret | Ret | 6 |
| 13 | | 5 | 4 | Ret | 7 | 7 | Ret | Ret | Ret | 6 | 8 | 6 |
| 14 | | Ret | 4 | Ret | 11 | Ret | 14 | Ret | 3 | |||
| 15 | | Ret | 7 | Ret | 6 | Ret | 7 | 1 | ||||
| 16 | | 9 | Ret | Ret | 11 | Ret | 8 | 6 | Ret | Ret | 7 | 1 |
| 17 | | Ret | 12 | Ret | 13 | Ret | 13 | Ret | 6 | 12 | 13 | 1 |
| 18 | | Ret | 10 | Ret | 15 | 10 | 12 | 12 | Ret | 7 | 6 | 1 |
| 19 | | 8 | Ret | 11 | 18 | 13 | Ret | 13 | 7 | Ret | 16 | 0 |
| 20 | | 7 | Ret | Ret | 16 | Ret | 10 | Ret | Ret | 13 | 12 | 0 |
| 21 | | Ret | Ret | 8 | 15 | 14 | 0 | |||||
| 22 | | Ret | 11 | 9 | 17 | 12 | 14 | Ret | Ret | Ret | 15 | 0 |
| 23 | | Ret | 9 | Ret | 0 | |||||||
| 24 | | Ret | 14 | 19 | 14 | Ret | Ret | 10 | Ret | 17 | 0 | |
| 25 | | Ret | 13 | Ret | 0 | |||||||
| 26 | | Ret | 14 | Ret | 0 |
| Rank | Name | Car | SUZ | MOT | MIN | FUJ | SUZ | SGO | FUJ | MIN | MOT | SUZ | Points |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | PIAA Nakajima | 64 | 2 | Ret | 3 | 1 | 2 | 1 | 1 | Ret | 3 | Ret | 81 |
| 65 | 3 | 1 | 8 | 10 | 5 | 11 | 4 | 1 | 5 | 9 | |||
| 2 | Unlimited LeMans | 1 | 1 | 2 | 1 | Ret | Ret | 2 | 3 | Ret | 1 | Ret | 52 |
| 2 | DNS | DNS | 4 | 4 | 8 | 9 | 8 | Ret | Ret | Ret | |||
| 3 | Be Brides Impul | 19 | Ret | Ret | 6 | 12 | 1 | Ret | Ret | Ret | 4 | 4 | 24 |
| 20 | Ret | 16 | 13 | 14 | 6 | Ret | Ret | 2 | 9 | 11 | |||
| 4 | Shionogi Nova | 9 | Ret | 3 | 2 | 9 | Ret | 6 | 10 | 9 | 8 | 1 | 22 |
| 10 | Ret | 10 | Ret | 15 | 10 | 12 | 12 | Ret | 7 | 6 | |||
| 5 | 5ZIGEN | 5 | Ret | 9 | Ret | 4 | Ret | 11 | Ret | 14 | Ret | 21 | |
| 6 | Ret | 5 | Ret | 3 | 11 | 4 | 9 | 4 | Ret | 2 | |||
| 6 | ARTA | 55 | 9 | Ret | Ret | 11 | Ret | 8 | 6 | Ret | Ret | 7 | 17 |
| 56 | Ret | 15 | 10 | Ret | 9 | 5 | 2 | 3 | 11 | 3 | |||
| 7 | Team LeyJun | 62 | 4 | 6 | 5 | 2 | Ret | Ret | 5 | 5 | 10 | 10 | 16 |
| 63 | Ret | 14 | Ret | Ret | Ret | 8 | 15 | 14 | |||||
| 8 | Team TMS | 17 | Ret | 7 | Ret | 6 | Ret | 7 | 11 | ||||
| 18 | Ret | Ret | 12 | 5 | 3 | 3 | |||||||
| 9 | Speedmaster Mooncraft | 14 | 6 | 8 | 7 | 8 | Ret | Ret | 7 | Ret | 2 | 5 | 10 |
| 15 | Ret | 12 | Ret | 13 | Ret | 13 | Ret | 6 | 12 | 13 | |||
| 10 | Cosmo Oil Cerumo | 11 | 5 | 4 | Ret | 7 | 7 | Ret | Ret | Ret | 6 | 8 | 6 |
| 12 | 7 | Ret | Ret | 16 | Ret | 10 | Ret | Ret | 13 | 12 | |||
| 11 | Asahi Kiko Sports | 3 | 8 | Ret | 11 | 18 | 13 | Ret | 13 | 7 | Ret | 16 | 0 |
| 12 | DoCoMo Dandelion | 68 | Ret | 11 | 9 | 17 | 12 | 14 | Ret | Ret | Ret | 15 | 0 |
| 13 | Takagi B-1 Racing | 36 | Ret | 14 | 19 | 14 | Ret | Ret | 10 | Ret | 17 | 0 | |
| 14 | Mirai | 32 | Ret | 13 | Ret | 0 |