| RD | Pick | Team | Player, Position | School
| 1 | 1 | Astros | Brady Aiken, LHP | Cathedral Catholic HS
| 1 | 2 | Marlins | Tyler Kolek, RHP | Shepherd HS
| 1 | 3 | White Sox | Carlos Rodon, LHP | NC State
| 1 | 4 | Cubs | Kyle Schwarber, C | Indiana
| 1 | 5 | Twins | Nick Gordon, SS | Olympia HS
| 1 | 6 | Mariners | Alex Jackson, C/OF | Rancho Bernardo HS
| 1 | 7 | Phillies | Aaron Nola, RHP | LSU
| 1 | 8 | Rockies | Kyle Freeland, LHP | Evansville
| 1 | 9 | Blue Jays | Jeff Hoffman, RHP | East Carolina
| 1 | 10 | Mets | Michael Conforto, OF | Oregon State
| 1 | 11 | Blue Jays | Max Pentecost, C | Kennesaw State
| 1 | 12 | Brewers | Kodi Medeiros, LHP | Waiakea HS
| 1 | 13 | Padres | Trea Turner, SS | NC State
| 1 | 14 | Giants | Tyler Beede, RHP | Vanderbilt
| 1 | 15 | Angels | Sean Newcomb, LHP | Hartford
| 1 | 16 | Diamondbacks | Touki Toussaint, RHP | Coral Springs Christian Academy
| 1 | 17 | Royals | Brandon Finnegan, LHP | TCU
| 1 | 18 | Nationals | Erick Fedde, RHP | UNLV
| 1 | 19 | Reds | Nick Howard, RHP | Virginia
| 1 | 20 | Rays | Casey Gillaspie, 1B | Wichita State
| 1 | 21 | Indians | Bradley Zimmer, OF | San Francisco
| 1 | 22 | Dodgers | Grant Holmes, RHP | Conway HS
| 1 | 23 | Tigers | Derek Hill, OF | Elk Grove HS
| 1 | 24 | Pirates | Cole Tucker, SS | Mountain Pointe HS
| 1 | 25 | Athletics | Matt Chapman, 3B | Cal State Fullerton
| 1 | 26 | Red Sox | Michael Chavis, SS | Sprayberry HS
| 1 | 27 | Cardinals | Luke Weaver, RHP | Florida State
| 1 | 28 | Royals | Foster Griffin, LHP | First Academy
| 1 | 29 | Reds | Alex Blandino, 3B | Stanford