The 2006 Cooper Tires Formula Ford 2000 Championship Series was the sixth and final season of the USF2000 Ford Zetec championship. It proved to be the ultimate USF2000 championship until the relaunch in 2010. J.R. Hildebrand won the championship in a Cape Motorsports entered Van Diemen RF05.
| Rank | Driver | ATL1 | ATL2 | MOH1 | MOH2 | PIR1 | PIR2 | CLE1 | CLE2 | TOR1 | TOR1 | MOH3 | MOH4 | ROA1 | ROA2 | Points |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 1 | 13 | 1 | 381 |
| 2 | | 2 | 2 | 26 | 3 | 8 | 9 | 2 | 1 | 2 | 2 | 2 | 17 | 1 | 11 | 272 |
| 3 | | 3 | 7 | 6 | 13 | 5 | 22 | 4 | 3 | 3 | 3 | 3 | 4 | 3 | 5 | 233 |
| 4 | | 16 | 6 | 2 | 2 | 7 | 3 | 5 | 5 | 15 | 5 | 5 | 6 | 4 | 2 | 228 |
| 5 | | 5 | 17 | 3 | 21 | 21 | 7 | 3 | 11 | 5 | 8 | 4 | 3 | 23 | 6 | 176 |
| 6 | | 15 | 26 | 7 | 6 | 17 | 13 | 10 | 7 | 4 | 4 | 8 | 9 | 6 | 4 | 165 |
| 7 | | 7 | 24 | 27 | 11 | 6 | 6 | 8 | 8 | 7 | 2 | 5 | 8 | 150 | ||
| 8 | | 4 | 4 | 8 | 4 | 2 | 12 | 6 | 4 | 138 | ||||||
| 9 | | 24 | 28 | 11 | 7 | 11 | 10 | 12 | 10 | 6 | 14 | 6 | 5 | 21 | 25 | 121 |
| 10 | | 9 | 25 | 14 | 26 | 16 | 18 | 18 | 15 | 14 | 7 | 14 | 8 | 8 | 10 | 101 |
| 11 | | 25 | 8 | 12 | 14 | 11 | 12 | 9 | 7 | 16 | 9 | 92 | ||||
| 12 | | 4 | 5 | 4 | 4 | 74 | ||||||||||
| 13 | | 8 | 5 | 17 | 8 | 9 | 6 | 18 | 20 | 74 | ||||||
| 14 | | 14 | 19 | 25 | 28 | 17 | 16 | 7 | 9 | 12 | 13 | 15 | 22 | 69 | ||
| 15 | | 22 | 16 | 7 | 8 | 16 | 6 | 9 | 27 | 62 | ||||||
| 16 | | 6 | 15 | 13 | 9 | 20 | 8 | 26 | 30 | 24 | 24 | 58 | ||||
| 17 | | 13 | 14 | 23 | 16 | 19 | 11 | 13 | 14 | 13 | 18 | 27 | DNS | 52 | ||
| 18 | | 28 | 12 | 28 | 27 | 30 | 26 | 8 | 10 | 15 | 12 | 52 | ||||
| 19 | | 23 | 20 | 19 | 19 | 15 | 18 | 10 | 12 | 11 | 14 | 52 | ||||
| 20 | | 11 | 9 | 24 | 24 | 23 | 16 | 29 | 19 | 18 | 18 | 10 | 17 | 50 | ||
| 21 | | 3 | 2 | 47 | ||||||||||||
| 22 | | 2 | 3 | 47 | ||||||||||||
| 23 | | 20 | 3 | 5 | 25 | 41 | ||||||||||
| 24 | | 21 | 27 | 9 | 10 | 12 | 26 | 21 | 25 | 37 | ||||||
| 25 | | 10 | 10 | 9 | 20 | 35 | ||||||||||
| 26 | | 25 | 24 | 25 | 13 | 13 | 16 | 18 | 10 | 34 | ||||||
| 27 | | 17 | 22 | 18 | 17 | 19 | 24 | 12 | 11 | 34 | ||||||
| 28 | | 27 | 11 | 26 | 17 | 16 | 20 | 17 | 15 | 29 | ||||||
| 29 | | 10 | 5 | 28 | ||||||||||||
| 30 | | 7 | 7 | 28 | ||||||||||||
| 31 | | 13 | 15 | 31 | 31 | 14 | ||||||||||
| 32 | | 14 | 14 | 14 | ||||||||||||
| 33 | | 17 | 12 | 13 | ||||||||||||
| 34 | | 27 | 25 | 19 | 19 | 30 | 15 | 9 | ||||||||
| 35 | | 15 | 21 | 7 | ||||||||||||
| 36 | | 18 | 27 | 4 | ||||||||||||
| 37 | | 22 | 22 | 22 | 28 | 4 | ||||||||||
| 38 | | 22 | 23 | 2 | ||||||||||||
| | 25 | 23 | ||||||||||||||
| | 19 | 18 | 15 | 23 | 20 | 29 | ||||||||||
| | 18 | 21 | 21 | 20 | 27 | 21 | 11 | 17 | ||||||||
| | 26 | 23 | 20 | 18 | 24 | 22 | 18 | 26 | ||||||||
| | 12 | 13 | 10 | 12 | 24 | 19 | 14 | 17 | 10 | 11 | 11 | 29 | ||||
| | 16 | 15 | 28 | 23 | 9 | 13 | 16 | 15 | ||||||||
| | 28 | 28 |