| Pick # | Round 1 | Pick # | Round 2 | Pick # | Round 3 | |
| 1 | Lon- | 1 | Lon- | 1 | Lon- | |
| Lon | Bryce Harper | Lon | Robbie Ross | Lon | Matt Dominguez | |
| 2 | Yk- | 2 | Alb- | 2 | Alb- | |
| Mun | Manny Machado | Mun | Jean Segura | Mun | Brett Jackson | |
| 3 | NE- | 3 | Can- | 3 | NE- | |
| SL | Matt Moore | SL | Hisashi Iwakuma | SL | Steve Lombardozzi | |
| 4 | Gle- | 4 | EY- | 4 | Gle- | |
| Gle | Yoenis Cespedes | Gle | Wily Peralta | Gle | Pedro Ciriaco | |
| 5 | Mun- | 5 | Yk- | 5 | Mun- | |
| Yk | Yu Darvish | Yk | Zack Cozart | Yk | Patrick Corbin | |
| 6 | IN- | 6 | IN- | 6 | Cro- | |
| Cro | Andrelton Simmons | Cro | Ryan Cook | Cro | Junichi Tazawa | |
| 7 | Cre- | 7 | Kal- | 7 | Alb- | |
| Can | Jarrod Parker | Can | Jordan Pacheco | Can | Drew Pomeranz | |
| 8 | SL- | 8 | Pa- | 8 | NE- | |
| NE | Wade Miley | NE | Michael Fiers | NE | Addison Reed | |
| 9 | Pa- | 9 | Dun- | 9 | Pa- | |
| Pa | Tommy Milone | Pa | V.Chris Carter | Pa | Joe Kelly | |
| 10 | Dun- | 10 | GM- | 10 | Yk- | |
| Dun | Wilin Rosario | Dun | Jacob Turner | Dun | Derek Norris | |
| 11 | GM- | 11 | NH- | 11 | GM- | |
| GM | Starling Marte | GM | Jose Quintana | GM | Wellington Castillo | |
| 12 | NH- | 12 | Can- | 12 | NH- | |
| NH | Josh Rutledge | NH | Donovan Solano | NH | Troy Patton | |
| 13 | Lex- | 13 | Lex- | 13 | Lex- | |
| Lex | Will Middlebrooks | Lex | Matt Carpenter | Lex | Ryan Lavarnway | |
| 14 | Can- | 14 | Cre- | 14 | Cre- | |
| Cre | Scott Diamond | Cre | Rob Brantly | Cre | Tyler Moore | |
| 15 | Mun- | 15 | Alb- | 15 | Alb- | |
| Alb | Norichika Aoki | Alb | Leonys Martin | Alb | J.J.Hoover | |
| 16 | GB- | 16 | GB- | 16 | GB- | |
| GB | Matt Harvey | GB | Adeiny Hechavarria | GB | Mark Rogers | |
| 17 | Cle- | 17 | Cle- | 17 | Cle- | |
| Cle | Brandon Belt | Cle | Randall Delgado | Cle | Hector Santiago | |
| 18 | Can- | 18 | Gle- | 18 | MC- | |
| MC | Drew Smyly | MC | Miguel Gonzalez | MC | Sean Doolittle | |
| 19 | IN- | 19 | IN- | 19 | IN- | |
| IN | Wei-Yin Chen | IN | Nate Jones | IN | Tyler Pastornicky | |
| 20 | VT- | 20 | EY- | 20 | GM- | |
| VT | A.J.Griffin | VT | Devin Mescoraco | VT | Ryan Mattheus | |
| 21 | Key- | 21 | Key- | 21 | Key- | |
| Key | Yasmani Grandal | Key | Erasmo J. Ramirez | Key | George Kontos | |
| 22 | Kal- | 22 | Kal- | 22 | Kal- | |
| Kal | Adam C. Eaton | Kal | Zach McAllister | Kal | Brad Brach | |
| 23 | NY- | 23 | NY- | 23 | NY- | |
| NY | Lucas Harrell | NY | David Phelps | NY | Cole De Vries | |
| 24 | SL- | 24 | Gle- | 24 | EY- | |
| EY | Kelvin Herrera | EY | Jared Hughes | EY | Brad Lincoln | |
| Rookie Draft pg 1 | ||||||
| Pick # | Round 4 | Pick # | Round 5 | |||
| 1 | Lon- | 1 | Key- | 2013 | Rookie | |
| Lon | Josh Donaldson | Lon | Mike Baxter | Draft | ||
| 2 | Mun- | 2 | Mun- | |||
| Mun | Martin Maldonado | Mun | Dale Thayer | 9:00 AM | ||
| 3 | Cle- | 3 | SL- | 2/23/2013 | ||
| SL | Hector Sanchez | SL | Sam Deduno | |||
| 4 | MC- | VT- | ||||
| Gle | Josh Vitters | Gle | Cody Eppley | |||
| 5 | Alb- | 5 | Yk- | 77 batters | ||
| Yk | Garrett Richards | Yk | Michael Kirkman | 95 pitchers | ||
| 6 | Cro- | 6 | NE- | (52 residual) | ||
| Cro | Freddy Galvis | Cro | Pedro Florimon | |||
| 7 | Can- | 7 | MC- | |||
| Can | Steve Clevenger | Can | Brock Holt | |||
| 8 | NE- | 8 | Cle- | |||
| NE | Fenando Martinez | NE | Michael Bowden | |||
| 9 | Pa- | 9 | Pa- | |||
| Pa | Travis Blackley | Pa | Erik Kratz | |||
| 10 | Dun- | 10 | VT- | |||
| Dun | Cody Allen | Dun | Jeremy Hefner | |||
| 11 | Dun- | 11 | GM- | |||
| GM | Stephen Pryor | GM | Marwin Gonzalez | |||
| 12 | NH- | 12 | MC- | |||
| NH | Matt Adams | NH | Christian Friedrich | |||
| 13 | Lex- | 13 | Lex- | |||
| Lex | Francisley Bueno | Lex | Dallas Keuchel | |||
| 14 | Cre- | 14 | Cre- | |||
| Cre | Jim Miller | Cre | Darin Mastroianni | |||
| 15 | Alb- | 15 | Alb- | |||
| Alb | Anthony Gose | Alb | Kole Calhoun | |||
| 16 | GB- | 16 | GB- | |||
| GB | Pete Kozma | GB | Miles Mikolas | |||
| 17 | Cle- | 17 | Cle- | |||
| Cle | Alex White | Cle | Dan Jennings | |||
| 18 | NE- | 18 | Gle- | |||
| MC | Steve Delabar | MC | Michael Schwimmer | |||
| 19 | IN- | 19 | IN- | |||
| IN | Quintin Berry | IN | Brian Dozier | |||
| 20 | Dun- | 20 | NE- | |||
| VT | Liam Hendriks | VT | Xavier Cedeno | |||
| 21 | Key- | 21 | Key- | |||
| Key | Evan Scribner | Key | Alberto Cabrera | |||
| 22 | Kal- | 22 | Kal- | |||
| Kal | Adam Ottavino | Kal | Lucas Luetge | |||
| 23 | NY- | 23 | NY- | |||
| NY | Kirk Nieuwenhuis | NY | Jordany Valdespin | |||
| 24 | Gle- | 24 | Pa- | |||
| EY | Jeremy Horst | EY | Duane Below | |||
| Rookie Draft page 2 |