The 2006 Formula Nippon Championship was contested over nine rounds, with twelve teams and 25 drivers competing in the championship. The specification chassis was the Lola FN06.
After eight seasons of a specification engine, there was a competition between engine manufacturers, as teams could choose between Toyota and Honda 3000cc Indy Racing League style specification normally aspirated engines.
| Round | Circuit | Date | Pole Position | Fastest Lap | Winning Driver | Winning Team |
|---|---|---|---|---|---|---|
| 1 | Fuji Speedway | 2 April |  Benoît Tréluyer |  Masataka Yanagida | Benoît Tréluyer | mobilecast IMPUL |
| 2 | Suzuka Circuit | 16 April | Benoît Tréluyer | Benoît Tréluyer | Loïc Duval | PIAA Nakajima |
| 3 | Twin Ring Motegi | 28 May | Takashi Kogure | Tsugio Matsuda |  André Lotterer | DHG TOM'S |
| 4 | Suzuka Circuit | 9 July | Benoît Tréluyer | Benoît Tréluyer | Benoît Tréluyer | mobilecast IMPUL |
| 5 | Autopolis | 6 August | Takashi Kogure | Loïc Duval | Tsugio Matsuda | mobilecast IMPUL |
| 6 | Fuji Speedway | 27 August | Takashi Kogure | Satoshi Motoyama | Benoît Tréluyer | mobilecast IMPUL |
| 7 | Sportsland SUGO | 17 September | Takashi Kogure | Hideki Mutoh | Loïc Duval | PIAA Nakajima |
| 8 | Twin Ring Motegi | 22 October | Takashi Kogure | Satoshi Motoyama | Benoît Tréluyer | mobilecast IMPUL |
| 9 | Suzuka Circuit | 19 November | Tsugio Matsuda | Benoît Tréluyer | André Lotterer | DHG TOM'S |
| Position | 1st | 2nd | 3rd | 4th | 5th | 6th |
|---|---|---|---|---|---|---|
| Points | 10 | 6 | 4 | 3 | 2 | 1 |
| Rank | Name | FUJ ‡ | SUZ | MOT | SUZ | ATP | FUJ | SGO | MOT | SUZ | Points |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Benoît Tréluyer | 1 | 3 | 2 | 1 | 7 | 1 | 2 | 1 | Ret | 51 |
| 2 | Tsugio Matsuda | 2 | 9 | 5 | 2 | 1 | 7 | 3 | 2 | 2 | 37 |
| 3 | André Lotterer | 8 | 5 | 1 | 5 | 8 | 2 | Ret | Ret | 1 | 30 |
| 4 | Loïc Duval | 11 | 1 | 6 | Ret | 18 | 9 | 1 | 4 | 6 | 25 |
| 5 | Satoshi Motoyama | 3 | 8 | 3 | 3 | Ret | 3 | 5 | Ret | Ret | 16 |
| 6 |  Björn Wirdheim | 4 | 2 | 4 | Ret | 6 | 6 | 6 | 11 | 9 | 13.5 |
| 7 | Tatsuya Kataoka | 13 | 7 | Ret | 6 | 3 | Ret | 9 | 3 | 3 | 13 |
| 8 | Yuji Tachikawa | 12 | Ret | 10 | 4 | 4 | 5 | 7 | 5 | Ret | 10 |
| 9 | Toshihiro Kaneishi | 16 | Ret | Ret | Ret | 2 | 4 | Ret | Ret | 7 | 9 |
| 10 |  Ronnie Quintarelli | 5 | Ret | Ret | Ret | 5 | 10 | 4 | 9 | 12 | 6 |
| 11 | Sakon Yamamoto | 6 | 4 | 14 | 3.5 | ||||||
| 12 | Takashi Kogure | 10 | 17 | Ret | 9 | 19 | Ret | DSQ | Ret | 4 | 3 |
| 13 | Takeshi Tsuchiya | 9 | 10 | Ret | 7 | 9 | Ret | 8 | 8 | 5 | 2 |
| 14 | Hideki Mutoh | 19 | 6 | 8 | Ret | 17 | 16 | 10 | 10 | Ret | 1 |
| 15 | Masataka Yanagida | 7 | Ret | 9 | 13 | 13 | 12 | Ret | 6 | 13 | 1 |
| 16 | Ryo Michigami | 20 | 18 | 7 | Ret | 11 | 15 | 12 | Ret | 11 | 0 |
| 17 | Naoki Yokomizo | 14 | 13 | Ret | 11 | Ret | Ret | 11 | 7 | Ret | 0 |
| 18 | Toranosuke Takagi | 22 | 16 | 11 | 8 | 16 | 8 | Ret | Ret | Ret | 0 |
| 19 |  João Paulo de Oliveira | 8 | 0 | ||||||||
| 20 | Seiji Ara | 10 | 10 | 18 | 13 | Ret | Ret | 0 | |||
| 21 | Yuji Ide | 12 | 12 | 11 | Ret | Ret | 10 | 0 | |||
| 22 | Katsuyuki Hiranaka | 17 | 11 | Ret | 15 | 14 | Ret | Ret | Ret | 0 | |
| 23 | Ryo Orime | 21 | 15 | 12 | Ret | Ret | 17 | DSQ | 12 | 0 | |
| 24 | Shogo Mitsuyama | 15 | 12 | 13 | Ret | 0 | |||||
| 25 | Kazuki Hoshino | 18 | 14 | Ret | Ret | 14 | 13 | Ret | Ret | 14 | 0 |
Note:
‡ Because of heavy rain at Fuji during the race, the event ended after two laps. Half points were awarded because of the stoppage before the 75% point.
| Rank | Team | Car | FUJ ‡ | SUZ | MOT | SUZ | ATP | FUJ | SGO | MOT | SUZ | Points |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | mobilecast Impul | 19 | 1 | 3 | 2 | 1 | 7 | 1 | 2 | 1 | Ret | 88 |
| 20 | 2 | 9 | 5 | 2 | 1 | 7 | 3 | 2 | 2 | |||
| 2 | DHG TOM'S | 36 | 8 | 5 | 1 | 5 | 8 | 2 | Ret | Ret | 1 | 32 |
| 37 | 9 | 10 | Ret | 7 | 9 | Ret | 8 | 8 | 5 | |||
| 3 | PIAA Nakajima | 31 | 11 | 1 | 6 | Ret | 18 | 9 | 1 | 4 | 6 | 26 |
| 32 | 19 | 6 | 8 | Ret | 17 | 16 | 10 | 10 | Ret | |||
| 4 | arting Impul | 1 | 3 | 8 | 3 | 3 | Ret | 3 | 5 | Ret | Ret | 16 |
| 2 | 18 | 14 | Ret | Ret | 14 | 13 | Ret | Ret | 14 | |||
| 5 | DoCoMo Dandelion | 40 | 4 | 2 | 4 | Ret | 6 | 6 | 6 | 11 | 9 | 13.5 |
| 41 | 17 | 11 | Ret | 12 | 12 | 11 | Ret | Ret | 10 | |||
| 6 | Team LeMans | 7 | 13 | 7 | Ret | 6 | 3 | Ret | 9 | 3 | 3 | 13 |
| 8 | 22 | 16 | 11 | 8 | 16 | 8 | Ret | Ret | Ret | |||
| 7 | ARTA | 55 | 16 | Ret | Ret | Ret | 2 | 4 | Ret | Ret | 7 | 12 |
| 56 | 10 | 17 | Ret | 9 | 19 | Ret | DSQ | Ret | 4 | |||
| 8 | Reckless Cerumo | 11 | 12 | Ret | 10 | 4 | 4 | 5 | 7 | 5 | Ret | 10 |
| 9 | BOSS INGING | 33 | 5 | Ret | Ret | Ret | 5 | 10 | 4 | 9 | 12 | 6 |
| 34 | 14 | 13 | Ret | 11 | Ret | Ret | 11 | 7 | Ret | |||
| 10 | Kondo Racing | 3 | 6 | 4 | 14 | 10 | 10 | 18 | 13 | Ret | Ret | 4.5 |
| 4 | 7 | Ret | 9 | 13 | 13 | 12 | Ret | 6 | 13 | |||
| 11 | Team 5ZIGEN | 5 | 20 | 18 | 7 | Ret | 11 | 15 | 12 | Ret | 11 | 0 |
| 6 | 21 | 15 | 12 | Ret | Ret | 17 | DSQ | 12 | 8 | |||
| 12 | DPR Direxiv | 27 | 15 | 12 | 13 | Ret | 0 |
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