| Pick # | Team | Player | Pick # | Team | Player | Pick # | Team | Player | ||
| 10 | ADD | Dan Straily | 11 | BCD | David Dahl | 3 | BEV | Trevor Story | ||
| 24 | ADD | Juan Nicasio | 15 | BCD | Tyler Glasnow | 22 | BEV | Keon Broxton | ||
| 38 | ADD | Hunter Cervenka | 21 | BCD | Albert Almora | 36 | BEV | Ryan Schimpf | ||
| 66 | ADD | Michael Bourn# | 49 | BCD | AJ Cole | 41 | BEV | Carl Edwards, Jr. | ||
| 80 | ADD | Jake Peavy | 56 | BCD | Sammy Solis | 50 | BEV | AJ Schugel | ||
| 94 | ADD | Ross Ohlendorf | 63 | BCD | Jhan Marinez | 64 | BEV | Aroldis Chapman# | ||
| 108 | ADD | Enrique Hernandez | 91 | BCD | Cory Gearrin | 69 | BEV | Jeremy Hazelbaker | ||
| 117 | ADD | Ivan De Jesus | 95 | BCD | Ryan Raburn | 78 | BEV | Aaron Hill | ||
| 122 | ADD | Aaron Blair | 105 | BCD | Adam Liberatore | 92 | BEV | Erick Aybar | ||
| 136 | ADD | Jordan Lyles | 119 | BCD | Chris Taylor | 106 | BEV | Josh Smith# | ||
| 150 | ADD | Jim Henderson | 133 | BCD | Rickie Weeks# | 120 | BEV | Hector Sanchez | ||
| 162 | ADD | Cody Asche# | 147 | BCD | Lucas Harrell# | 134 | BEV | Gonzalez Germen | ||
| 170 | ADD | Brett Wallace | 160 | BCD | Tyler Goeddel | 148 | BEV | Jose Dominguez | ||
| 176 | ADD | Alex Presley# | ||||||||
| Pick # | Team | Player | Pick # | Team | Player | Pick # | Team | Player | ||
| 5 | BGN | Aledmys Diaz | 1 | GAL | Dansby Swanson | 12 | GRC | Junior Guerra | ||
| 25 | BGN | Seth Lugo | 43 | GAL | Tommy Joseph | 14 | GRC | Alex Reyes | ||
| 32 | BGN | Colin Rea | 57 | GAL | Jorge de la Rosa | 23 | GRC | Andrew Toles | ||
| 46 | BGN | Mauricio Cabrera | 74 | GAL | Blake Wood | 26 | GRC | Manuel Margot | ||
| 51 | BGN | Jake Barrett | 85 | GAL | Gregor Blanco | 37 | GRC | Scott Schebler | ||
| 83 | BGN | Jarred Cosart | 99 | GAL | Roman Quinn | 40 | GRC | Derek Law | ||
| 88 | BGN | Chris Heisey | 112 | GAL | Mike Dunn | 61 | GRC | Daniel Hudson | ||
| 114 | BGN | Eric Fryer | 113 | GAL | Grant Dayton | 82 | GRC | Chris Stewart | ||
| 130 | BGN | Williams Perez | 127 | GAL | Ramon Flores# | 110 | GRC | Carlos Estevez | ||
| 144 | BGN | Erik Goeddel | 141 | GAL | Jonathan Papelbon | 124 | GRC | John Gant | ||
| 158 | BGN | Scott Van Slyke | 155 | GAL | Ramon Cabrera | 138 | GRC | Ty Kelly | ||
| 169 | BGN | Mitch Haniger# | 167 | GAL | Brandon Barnes | 152 | GRC | Chris Hatcher | ||
| 175 | BGN | Cesar Vargas | 174 | GAL | Josh Osich | 164 | GRC | Andre Ethier | ||
| 180 | BGN | Enrique Burgos | ||||||||
| Pick # | Team | Player | Pick # | Team | Player | Pick # | Team | Player | ||
| 17 | HOL | Jose Peraza | 35 | JER | Ryan Buchter | 2 | LAK | Kenta Maeda | ||
| 42 | HOL | Alex Dickerson | 39 | JER | Matt Bowman | 6 | LAK | Seung Hwan Oh | ||
| 54 | HOL | Clayton Richard | 53 | JER | Adam Frazier | 16 | LAK | Orlando Arcia | ||
| 70 | HOL | Adam Ottavino | 58 | JER | TJ Rivera | 30 | LAK | Chad Kuhl | ||
| 71 | HOL | Rene Rivera | 96 | JER | Jabari Blash | 44 | LAK | Brandon McCarthy | ||
| 77 | HOL | Braden Shipley | 107 | JER | Edubray Ramos | 52 | LAK | David Ross | ||
| 98 | HOL | Brad Ziegler | 109 | JER | Jake McGee | 86 | LAK | Will Smith | ||
| 126 | HOL | Keyvius Sampson | 123 | JER | Zack Duke | 100 | LAK | Jhoulys Chacin | ||
| 140 | HOL | Socrates Brito | 137 | JER | Alfredo Simon | 102 | LAK | Tyler Cravy | ||
| 154 | HOL | Rob Scahill | 151 | JER | Brett Oberholtzer# | 116 | LAK | Joel de la Cruz | ||
| 166 | HOL | Chris Capuano | 163 | JER | Steve Selsky# | 142 | LAK | Tyrell Jenkins | ||
| 173 | HOL | Jimmy Paredes | 171 | JER | Yadiel Rivera | 156 | LAK | Ryan Howard | ||
| 179 | HOL | Jason Motte | 177 | JER | Andrew Bailey# | 168 | LAK | Gorkys Hernandez | ||
| 182 | HOL | Ryan Weber# | 181 | JER | Kyle Lobstein | |||||
| 183 | JER | Brock Stewart | ||||||||
| Pick # | Team | Player | Pick # | Team | Player | Pick # | Team | Player | ||
| 9 | MAN | Julio Urias | 4 | MIL | Willson Contreras | 7 | ORL | Tony Wolters | ||
| 18 | MAN | Hunter Renfroe | 31 | MIL | **Penalty** | 20 | ORL | Ross Stripling | ||
| 55 | MAN | Jeff Hoffman | 45 | MIL | Brandon Nimmo | 34 | ORL | Albert Suarez | ||
| 65 | MAN | Matt Belisle# | 59 | MIL | Zack Eflin | 48 | ORL | Trevor Brown | ||
| 79 | MAN | Luke Weaver | 67 | MIL | Arodys Vizcaino | 62 | ORL | Santiago Casilla# | ||
| 93 | MAN | Jerry Blevins | 68 | MIL | Tommy La Stella | 76 | ORL | Mallix Smeth# | ||
| 121 | MAN | Chris Coghlan | 73 | MIL | Mac Williamson | 90 | ORL | Nick Wittgren | ||
| 135 | MAN | Manny Pina | 84 | MIL | Paul Clemens | 97 | ORL | Kevin Quackenbush | ||
| 149 | MAN | Jose Ramirez | 87 | MIL | Daniel Castro | 104 | ORL | Wilmer Difo | ||
| 161 | MAN | Clint Robinson | 101 | MIL | Jacob Barnes | 118 | ORL | Chris Withrow# | ||
| 115 | MIL | Brian Ellington | 132 | ORL | Ramiro Pena | |||||
| 129 | MIL | Tyler Holt | 146 | ORL | Reynaldo Lopez# | |||||
| 143 | MIL | Stephen Brault | ||||||||
| 157 | MIL | Matt Reynolds | ||||||||
| Pick # | Team | Player | Pick # | Team | Player | |||||
| 8 | TUX | Jameson Taillon | 19 | WES | Tyler Anderson | |||||
| 13 | TUX | **Penalty** | 28 | WES | Josh Bell | |||||
| 27 | TUX | Robert Gsellman | 29 | WES | Luis Perdomo | |||||
| 60 | TUX | Robert Stephenson | 33 | WES | Tim Adleman | |||||
| 81 | TUX | Matt Cain | 47 | WES | Jake Thompson | |||||
| 111 | TUX | Louis Coleman | 72 | WES | Cody Reed | |||||
| 125 | TUX | John Lamb# | 75 | WES | Dustin McGowan | |||||
| 139 | TUX | Oliver Perez | 89 | WES | Edwin Jackson | |||||
| 153 | TUX | Tyler Clippard# | 103 | WES | Chase d'Arnaud | |||||
| 165 | TUX | Severino Gonzalez | 128 | WES | Jose Lobaton | |||||
| 172 | TUX | Adam Warren# | 131 | WES | JP Howell# | |||||
| 178 | TUX | Justin Miller# | 145 | WES | Charlie Culberson | |||||
| 159 | WES | Dustin Garneau | ||||||||