2005 Expansion Draft Phase II
| Rd. | Pick | Team | Player | . | Rd. | Pick | Team | Player | . |
| 1 | 1 | SHS | CGuillen - SS | KEN 1 | 9 | 33 | SHS | JMichaels - OF | STL 2 |
| 1 | 2 | DUN | JCantu - 2B | NYK 1 | 9 | 34 | DUN | CGanderson - OF | WCB 3 |
| 1 | 3 | CHF | JWilson - SS | MMD 1 | 9 | 35 | CHF | BInge - 3B | MAN 2 |
| 1 | 4 | MER | LOverbay - 1B | NYK 2 | 9 | 36 | MER | ABoone - 3B | MMD 2 |
| 2 | 5 | SHS | MBarrett - C | PIT 1 | 10 | 37 | SHS | DWells - SP | EMO 1 |
| 2 | 6 | DUN | CCrisp - OF | MIL 1 | 10 | 38 | DUN | KWells - SP | WCB 4 |
| 2 | 7 | CHF | DNavarro - C | NYY 1 | 10 | 39 | CHF | AEaton - SP | MAN 3 |
| 2 | 8 | MER | ARios - OF | NYK 3 | 10 | 40 | MER | JJones - OF | MMD 3 |
| 3 | 9 | SHS | JGiambi - 1B/DH | MIL 2 | 11 | 41 | SHS | MGrudzielanek - 2B | WIC 2 |
| 3 | 10 | DUN | GAtkins - 3B | NYM 1 | 11 | 42 | DUN | RWolf - SP | MMD 4 |
| 3 | 11 | CHF | DMcPherson - 3B | NYM 2 | 11 | 43 | CHF | JReed - OF | MAN 4 |
| 3 | 12 | MER | JCastillo - 2B | PIT 2 | 11 | 44 | MER | MRedman - SP | WIC 3 |
| 4 | 13 | SHS | MClement - SP | NYK 4 | 12 | 45 | SHS | RBetancourt - RP | NYY 2 |
| 4 | 14 | DUN | WTavarez - OF | CON 1 | 12 | 46 | DUN | THoffman - RP | PIT 4 |
| 4 | 15 | CHF | JWeaver - SP | KEN 2 | 12 | 47 | CHF | AdGonzalez - 1B | CIF 3 |
| 4 | 16 | MER | ARowand - OF | CIF 1 | 12 | 48 | MER | ABenitez - SP | CIF 4 |
| 5 | 17 | SHS | MCameron - OF | BCE 1 | 13 | 49 | SHS | FCabrera - RP | STL 3 |
| 5 | 18 | DUN | JeWilliams - SP | NYM 3 | 13 | 50 | DUN | VDiaz - OF | EMO 2 |
| 5 | 19 | CHF | JGibbons - OF | WCB 1 | 13 | 51 | CHF | JLaRue - C | WIC 4 |
| 5 | 20 | MER | CPatterson - OF | NYM 4 | 13 | 52 | MER | GMota - RP | EMO 3 |
| 6 | 21 | SHS | RMadson - RP | STL 1 | 14 | 53 | SHS | CReitsma - RP | SSB 2 |
| 6 | 22 | DUN | JPiniero - SP | MAN 1 | 14 | 54 | DUN | GQuiroz - C | CON 2 |
| 6 | 23 | CHF | RBarajas - C | PIT 3 | 14 | 55 | CHF | RAdams - SS | CON 3 |
| 6 | 24 | MER | RIbanez - OF | SSB 1 | 14 | 56 | MER | OHernandez - SP | SSB 3 |
| 7 | 25 | SHS | RChurch - OF | KEN 3 | 15 | 57 | SHS | WMiller - SP | EMO 4 |
| 7 | 26 | DUN | JBuck - C | KEN 4 | 15 | 58 | DUN | AEverett - SS | CON 4 |
| 7 | 27 | CHF | LAGonzalez - 2B | MIL 3 | 15 | 59 | CHF | JMateo - RP | NYY 3 |
| 7 | 28 | MER | JBartlett - SS | BCE 2 | 15 | 60 | MER | AOtsuka - RP | NYY 4 |
| 8 | 29 | SHS | BMueller - 3B | WIC 1 | 16 | 61 | SHS | JGerut - OF | BCE 3 |
| 8 | 30 | DUN | VPadilla - SP | WCB 2 | 16 | 62 | DUN | TLee - 1B | BCE 4 |
| 8 | 31 | CHF | EHinske - 3B | MIL 4 | 16 | 63 | CHF | RJohnson - OF | SSB 4 |
| 8 | 32 | MER | RLopez - SP | CIF 2 | 16 | 64 | MER | MLowell - 3B | STL 4 |