| Year: | 2006 |
| Team: | Florida Atlantic Owls |
| Conference: | Sun Belt Conference |
| Short Conf: | Sun Belt |
| Record: | 5–7 |
| Conf Record: | 4–3 |
| Hc Year: | 6th |
| Oc Year: | 2nd |
| Def Coach: | Kirk Hoza |
| Dc Year: | 6th |
| Stadium: | Lockhart Stadium |
The 2006 Florida Atlantic University Owls football team represented Florida Atlantic University in the 2006 NCAA Division I FBS football season. The team was coached by Howard Schnellenberger[1] and played their home games at Lockhart Stadium in Fort Lauderdale, Florida. The Owls entered their first season as full members of the Sun Belt Conference. There was a battle for the starting quarterback position between freshman Rusty Smith and junior Sean Clayton. Throughout the season they split playing time.