| NAIA | ||||||||
| Football rankings | ||||||||
| Final rankings for 2006 season | ||||||||
| Rank | Team | Conference | W | L | Net | Score | Win | |
| 1 | Sioux Falls | Great Plains | 14 | 0 | 42.51 | 39.35 | 3.16 | |
| 2 | Saint Francis (IN) | Mid-States - Mideast | 13 | 1 | 34.99 | 33.91 | 1.08 | |
| 3 | Missouri Valley | Heart of America | 13 | 1 | 29.81 | 23.58 | 6.23 | |
| 4 | Northwestern (IA) | Great Plains | 11 | 2 | 28.00 | 28.05 | (0.05) | |
| 5 | Carroll (Montana) | Frontier | 11 | 2 | 25.87 | 20.03 | 5.84 | |
| 6 | Saint Xavier | Mid-States - Midwest | 10 | 3 | 25.41 | 23.72 | 1.69 | |
| 7 | Bethel (TN) | Mid-South | 10 | 3 | 23.17 | 28.01 | (4.84) | |
| 8 | Morningside | Great Plains | 9 | 3 | 23.06 | 16.98 | 6.08 | |
| 9 | Saint Ambrose | Mid-States - Midwest | 10 | 1 | 22.41 | 15.09 | 7.32 | |
| 10 | Georgetown (KY) | Mid-South | 9 | 2 | 21.40 | 21.66 | (0.26) | |
| 11 | Montana State - Northern | Frontier | 9 | 3 | 21.39 | 14.96 | 6.43 | |
| 12 | Langston | X - Independents (NAIA) | 5 | 4 | 20.94 | 23.81 | (2.87) | |
| 13 | Walsh | Mid-States - Mideast | 9 | 3 | 20.21 | 12.36 | 7.85 | |
| 14 | Ohio Dominican | Mid-States - Mideast | 7 | 3 | 17.43 | 15.12 | 2.31 | |
| 15 | Black Hills State | Dakota | 8 | 3 | 16.55 | 17.81 | (1.26) | |
| 16 | Friends | Kansas | 9 | 2 | 16.01 | 10.88 | 5.13 | |
| 17 | Malone | Mid-States - Mideast | 7 | 4 | 15.32 | 7.61 | 7.71 | |
| 18 | Bethel (KS) | Kansas | 9 | 2 | 14.87 | 6.82 | 8.05 | |
| 19 | Kansas Wesleyan | Kansas | 8 | 2 | 12.19 | 6.33 | 5.86 | |
| 20 | MidAmerica Nazarene | Heart of America | 7 | 3 | 11.98 | 11.90 | 0.08 | |
| 21 | Jamestown | Dakota | 8 | 3 | 11.55 | 11.91 | (0.36) | |
| 22 | Nebraska Wesleyan | Great Plains | 7 | 3 | 11.36 | 4.41 | 6.95 | |
| 23 | Benedictine (KS) | Heart of America | 8 | 3 | 11.27 | 6.71 | 4.56 | |
| 24 | Montana Tech | Frontier | 6 | 5 | 10.86 | 7.52 | 3.34 | |
| 25 | Virginia - Wise | Mid-South | 8 | 3 | 10.11 | 9.79 | 0.32 | |
| 26 | Graceland | Heart of America | 6 | 4 | 9.13 | 11.50 | (2.37) | |
| 27 | Cumberlands (KY) | Mid-South | 6 | 4 | 8.67 | 6.79 | 1.88 | |
| 28 | Sterling | Kansas | 7 | 3 | 8.42 | 6.80 | 1.62 | |
| 29 | McKendree | Mid-States - Midwest | 5 | 4 | 8.42 | 15.87 | (7.45) | |
| 30 | Eastern Oregon | Frontier | 6 | 5 | 7.96 | 3.56 | 4.40 | |
| 31 | NW Oklahoma State | Central States | 6 | 4 | 7.74 | 10.17 | (2.43) | |
| 32 | Azusa Pacific | X - Independents (NAIA) | 3 | 7 | 7.46 | 10.58 | (3.12) | |
| 33 | Urbana | Mid-States - Mideast | 5 | 6 | 7.41 | 7.44 | (0.03) | |
| 34 | Geneva | Mid-States - Mideast | 4 | 5 | 5.30 | 5.06 | 0.24 | |
| 35 | Webber International | X - Independents (NAIA) | 5 | 5 | 5.15 | 8.01 | (2.86) | |
| 36 | Quincy | Mid-States - Midwest | 6 | 5 | 4.23 | 7.48 | (3.25) | |
| 37 | Southern Oregon | X - Independents (NAIA) | 3 | 6 | 4.18 | 3.63 | 0.55 | |
| 38 | Dickinson State | Dakota | 6 | 4 | 4.12 | 6.30 | (2.18) | |
| 39 | Dana | Great Plains | 6 | 5 | 3.79 | 7.93 | (4.14) | |
| 40 | William Penn | Mid-States - Midwest | 5 | 6 | 3.65 | 3.88 | (0.23) | |
| 41 | Valley City State | Dakota | 6 | 4 | 2.85 | 4.36 | (1.51) | |
| 42 | William Jewell | Heart of America | 5 | 5 | 2.17 | 3.04 | (0.87) | |
| 43 | Southern Nazarene | Central States | 6 | 4 | 2.17 | 5.60 | (3.43) | |
| 44 | Shorter | Mid-South | 6 | 5 | 1.92 | 6.70 | (4.78) | |
| 45 | Lindenwood | Heart of America | 5 | 7 | 0.51 | 2.07 | (1.56) | |
| 46 | Belhaven | Mid-South | 6 | 5 | (0.19) | 5.28 | (5.47) | |
| 47 | Baker | Heart of America | 4 | 6 | (1.65) | 0.39 | (2.04) | |
| 48 | Evangel | Heart of America | 4 | 6 | (1.80) | (0.05) | (1.75) | |
| 49 | Minot State | Dakota | 4 | 6 | (1.88) | 6.45 | (8.33) | |
| 50 | Tabor | Kansas | 6 | 4 | (2.05) | (1.48) | (0.57) | |
| 51 | Hastings | Great Plains | 4 | 6 | (2.89) | 1.59 | (4.48) | |
| 52 | Texas College | Central States | 4 | 7 | (3.08) | 1.28 | (4.36) | |
| 53 | Trinity International | Mid-States - Midwest | 4 | 7 | (3.66) | (0.83) | (2.83) | |
| 54 | Dakota Wesleyan | Great Plains | 4 | 6 | (4.46) | (2.19) | (2.27) | |
| 55 | Lambuth | Mid-South | 4 | 7 | (4.60) | (1.23) | (3.37) | |
| 56 | Pikeville | Mid-South | 4 | 6 | (4.95) | (4.52) | (0.43) | |
| 57 | Paul Quinn | X - Independents (NAIA) | 2 | 6 | (5.84) | (5.37) | (0.47) | |
| 58 | Peru State | Central States | 6 | 5 | (6.00) | 0.54 | (6.54) | |
| 59 | Briar Cliff | Great Plains | 5 | 6 | (6.09) | (6.15) | 0.06 | |
| 60 | Olivet Nazarene | Mid-States - Midwest | 4 | 7 | (6.20) | (2.64) | (3.56) | |
| 61 | Seton Hill (PA) | Mid-States - Mideast | 2 | 9 | (7.85) | (6.07) | (1.78) | |
| 62 | Central Methodist | Heart of America | 3 | 8 | (8.09) | (3.36) | (4.73) | |
| 63 | Culver - Stockton | Heart of America | 3 | 8 | (8.35) | (6.05) | (2.30) | |
| 64 | Rocky Mountain | Frontier | 2 | 9 | (9.63) | (5.93) | (3.70) | |
| 65 | Avila | Heart of America | 3 | 8 | (10.15) | (6.52) | (3.63) | |
| 66 | Cumberland (TN) | Mid-South | 3 | 7 | (10.20) | (3.57) | (6.63) | |
| 67 | Concordia (AL) | X - Independents (NAIA) | 2 | 8 | (11.36) | (5.39) | (5.97) | |
| 68 | Campbellsville | Mid-South | 2 | 8 | (12.11) | (7.60) | (4.51) | |
| 69 | Montana - Western | Frontier | 1 | 9 | (12.62) | (3.80) | (8.82) | |
| 70 | Dakota State | Dakota | 3 | 8 | (13.20) | (8.79) | (4.41) | |
| 71 | Southern Virginia | X - Independents (NAIA) | 2 | 7 | (13.33) | (7.61) | (5.72) | |
| 72 | Union (KY) | Mid-South | 2 | 8 | (13.76) | (6.30) | (7.46) | |
| 73 | Concordia (Neb) | Great Plains | 2 | 8 | (14.73) | (4.57) | (10.16) | |
| 74 | Taylor | Mid-States - Mideast | 1 | 9 | (16.33) | (10.18) | (6.15) | |
| 75 | Midland Lutheran | Great Plains | 2 | 9 | (16.66) | (4.33) | (12.33) | |
| 76 | Edward Waters | X - Independents (NAIA) | 1 | 9 | (17.54) | (8.87) | (8.67) | |
| 77 | Doane | Great Plains | 1 | 9 | (18.06) | (7.38) | (10.68) | |
| 78 | Saint Mary (KS) | Kansas | 3 | 7 | (18.52) | (13.68) | (4.84) | |
| 79 | Waldorf | X - Independents (NAIA) | 2 | 8 | (19.14) | (10.91) | (8.23) | |
| 80 | SW Assemblies of God | X - Independents (NAIA) | 2 | 8 | (19.47) | (17.24) | (2.23) | |
| 81 | Ottawa | Kansas | 1 | 9 | (21.11) | (13.71) | (7.40) | |
| 82 | Southwestern | Kansas | 2 | 8 | (21.36) | (14.40) | (6.96) | |
| 83 | Bethany (KS) | Kansas | 2 | 8 | (21.56) | (14.99) | (6.57) | |
| 84 | McPherson | Kansas | 3 | 7 | (21.66) | (20.34) | (1.32) | |
| 85 | Iowa Wesleyan | Mid-States - Midwest | 1 | 9 | (21.79) | (15.58) | (6.21) | |
| 86 | West Virginia Tech | Mid-South | 1 | 10 | (22.47) | (17.32) | (5.15) | |
| 87 | Bacone | Central States | 1 | 9 | (22.65) | (17.90) | (4.75) | |
| 88 | Saint Francis (IL) | Mid-States - Midwest | 1 | 9 | (23.13) | (19.22) | (3.91) | |
| 89 | Haskell Indian Nations | X - Independents (NAIA) | 2 | 9 | (24.74) | (22.87) | (1.87) | |
| 90 | Mayville State | Dakota | 1 | 9 | (26.83) | (26.93) | 0.10 | |
| 91 | South Dakota Tech | Dakota | 1 | 9 | (27.99) | (28.87) | 0.88 | |