| Election Name: | 2006 Navajo Nation Election |
| Country: | Navajo Nation |
| Flag Image: | Navajo flag.svg |
| Type: | presidential |
| Ongoing: | no |
| Previous Election: | 2002 Navajo Nation presidential election |
| Previous Year: | 2002 |
| Next Election: | 2010 Navajo Nation presidential election |
| Next Year: | 2010 |
| Election Date: | 8 August 2006 (Primary) 6 November 2006 (Run off) |
| Image1: | Joe Shirley.jpg |
| Nominee1: | Joe Shirley Jr. |
| Color1: | 3333FF |
| Running Mate1: | Ben Shelly |
| Popular Vote1: | 34,945 |
| Percentage1: | 53.27% |
| Nominee2: | Lynda Lovejoy |
| Color2: | FF3333 |
| Running Mate2: | Walter Phelps |
| Popular Vote2: | 30,653 |
| Percentage2: | 46.73% |
| Map Size: | 350px |
| Before Election: | Joe Shirley Jr. |
| After Election: | Joe Shirley Jr. |
| President | |
| Posttitle: | President |
| 1Blank: | Home Town |
| 1Data1: | Chinle |
| 1Data2: | Crownpoint |
| 2Blank: | Chapters Carried |
| 2Data1: | 75 |
| 2Data2: | 0 |
The Navajo Nation Presidential elections took place on November 7, 2006. Primary elections took place on August 8, 2006. Incumbent President Joe Shirley Jr. was re-elected, defeating 11 candidates, including former New Mexico State senator Lynda Lovejoy.
Shirley Jr. (Chinle) and Lovejoy (Crownpoint) proceeded to a runoff in November 2007. This was he first time in Navajo government history that a woman made it to the runoff. Immediately after the first round, Mrs. Lovejoy selected Walter Phelps from Leupp, Arizona as her running mate to challenge Shirley, who picked Navajo Nation Council Delegate Ben Shelly (Thoreau).
Shirley defeated Lovejoy in the second round by a margin of 4,000. Becoming the first leader of the Navajo nation to be re-elected since Chairman Peter MacDonald.