| Year: | 2006 |
| Team: | Navy Midshipmen |
| Sport: | football |
| Conference: | Independent |
| Record: | 9–4 |
| Head Coach: | Paul Johnson |
| Hc Year: | 5th |
| Off Scheme: | Triple option |
| Def Coach: | Buddy Green |
| Dc Year: | 5th |
| Def Scheme: | Multiple |
| Mvp: | David Mahoney |
| Captain: | James Rossi |
| Captain2: | Rob Caldwell |
| Stadium: | Navy–Marine Corps Memorial Stadium |
| Bowl: | Meineke Car Care Bowl |
| Bowl Result: | L 24–25 vs. Boston College |
The 2006 Navy Midshipmen football team represented the United States Naval Academy (USNA) as an independent during the 2006 NCAA Division I FBS football season. The team was led by fifth-year head coach Paul Johnson.