| Club: | Miami FC |
| Season: | 2006 |
| Manager: | Chiquinho de Assis |
| Chairman: | Aaron Davidson |
| League: | USL First Division |
| League Result: | Fifth place |
| Cup1: | USL First Division playoffs |
| Cup1 Result: | First round |
| Cup2: | U.S. Open Cup |
| Cup2 Result: | Second round |
| League Topscorer: | Romário and Cam Weaver (18) |
| Pattern La1: | _navylower |
| Pattern B1: | _navyhorizontal |
| Pattern Ra1: | _navylower |
| Leftarm1: | 4169E1 |
| Body1: | 4169E1 |
| Rightarm1: | 4169E1 |
| Shorts1: | 000080 |
| Socks1: | 000080 |
| Pattern B2: | _goldhorizontal |
| Leftarm2: | ffffff |
| Body2: | ffffff |
| Rightarm2: | ffffff |
| Shorts2: | ffffff |
| Socks2: | ffffff |
| Prevseason: | 1997 Strikers |
| Nextseason: | 2007 Miami FC |
The 2006 Miami FC season was the first season of the new team and club in the USL First Division.This year, the team finished in fifth place for the regular season and made it to the first round of the playoffs.
| width=30 | Pos | width=200 | Club | width=30 | Pts | width=30 | Pld | width=30 | W | width=30 | L | width=30 | T | width=30 | GF | width=30 | GA | width=30 | GD | width=100 | H2H Pts |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Montreal Impact | 51 | 28 | 14 | 5 | 9 | 31 | 15 | +16 | ||||||||||||
| 2 | Rochester Raging Rhinos | 50 | 28 | 13 | 4 | 11 | 34 | 21 | +13 | ||||||||||||
| 3 | Charleston Battery | 46 | 28 | 13 | 8 | 7 | 33 | 25 | +8 | CHA: 4 pts VAN: 1 pt | |||||||||||
| 4 | Vancouver Whitecaps | 46 | 28 | 12 | 6 | 10 | 40 | 28 | +12 | ||||||||||||
| 5 | Miami FC | 39 | 28 | 11 | 11 | 6 | 47 | 44 | +3 | ||||||||||||
| 6 | Puerto Rico Islanders | 38 | 28 | 10 | 10 | 8 | 38 | 36 | +2 | ||||||||||||
| 7 | Seattle Sounders | 37 | 28 | 11 | 13 | 4 | 42 | 48 | −6 | ||||||||||||
| 8 | Atlanta Silverbacks | 35 | 28 | 10 | 13 | 5 | 36 | 42 | −6 | ||||||||||||
| 9 | Virginia Beach Mariners | 32 | 28 | 8 | 12 | 8 | 26 | 37 | −11 | VBM: 7 pts TOR: 4 pts | |||||||||||
| 10 | Toronto Lynx | 32 | 28 | 8 | 12 | 8 | 30 | 36 | −6 | ||||||||||||
| 11 | Portland Timbers | 27 | 28 | 7 | 15 | 6 | 25 | 39 | −14 | POR: 9 pts MIN: 3 pts | |||||||||||
| 12 | Minnesota Thunder | 27 | 28 | 7 | 15 | 6 | 34 | 45 | −11 |