| 1st Round | 4th Round | ||
| 1. Brad Miller | New York Yankees | 91. Tom Koehler | Chicago Cubs |
| 2. Mike Zunino | Detroit Tigers | 92. Chad Bettis | Detroit Tigers |
| 3. Travis d'Arnaud | Boston Red Sox | 93. Yusmeiro Petit | Atlanta Braves |
| 4. Kolton Wong | Boston Red Sox | 94. Jesse Chavez | Chicago White Sox |
| 5. Jackie Bradley Jr. | New York Mets | 95. Todd Redmond | Chicago Cubs |
| 6. Hyun-Jin Ryu | Pittsburgh Pirates | 96. Cameron Rupp | Atlanta Braves |
| 7. Christian Yelich | Texas Rangers | 97. Ryan Jackson | San Diego Padres |
| 8. Marcell Ozuna | Philadelphia Phillies | 98. Vic Black | New York Mets |
| 9. Matt Davidson | Houston Astros | 99. Russ Ohlendorf | Los Angeles Angels |
| 10. Nick Franklin | Atlanta Braves | 100. Stomly Pimental | Cincinnati Reds |
| 11. James Paxton | Cleveland Indians | 101. Donnie Veal | Cleveland Indians |
| 12. Alex Wood | Seattle Mariners | 102. Jake Elmore | Miami Marlins |
| 13. Carlos Martinez | Los Angeles Dodgers | 103. Jean Machi | Texas Rangers |
| 14. Jarred Cosart | Baltimore Orioles | 104. Nate Karns | Washington Nationals |
| 15. Khris Davis | Seattle Mariners | 105. Brandon Maurer | Philadelphia Phillies |
| 16. Michael Choice | Texas Rangers | 106. Kevin Gregg | Texas Rangers |
| 17. Josmil Pinto | Minnesota Twins | 107. Engel Beltre | St, Louis Cardinals |
| 18. Christian Bethancourt | Chicago White Sox | 108. Jose Dominguez | Detroit Tigers |
| 19. Jonathan Villar | Philadelphia Phillies | 109. Matt Tuaisosopo | Pittsburgh Pirates |
| 20. Kyle Gibson | Atlanta Braves | 110. Jake Diekman | Oakland A's |
| 21. Robbie Erlin | Los Angeles Dodgers | 111. Ramiro Pena | Chicago Cubs |
| 22. Corey Dickerson | Toronto Blue Jays | 112. Michael Kickham | San Francisco Giants |
| 23. Brandon Kintzler | Los Angeles Dodgers | 113. Brendan Harris | Washington Nationals |
| 24. Jimmy Nelson | Minnesota Twins | 114. Tommy Medica | San Diego Padres |
| 25. Juan Lagares | San Francisco Giants | 115. Michael Kohn | Texas Rangers |
| 26. Robbie Grossman | Atlanta Braves | 116. Ethan Martin | San Diego Padres |
| 27. Jake Marisnik | Detroit Tigers | 117. Leury Garcia | Milwaukee Brewers |
| 28. Bruce Rondon | New York Yankees | 118. David Hale | Chicago Cubs |
| 29. Danny Farquhar | Seattle Mariners | 119. Chad Qualls | Seattle Mariners |
| 30. Jonathan Schoop | Washington Nationals | 120. Rene Rivera | Washington Nationals |
| 2nd Round | 5th Round | ||
| 31. Jim Henderson | New York Mets | 121. Charlie Culberson | Baltimore Orioles |
| 32. Allen Webster | Detroit Tigers | 122. Donald Lutz | Cincinnati Reds |
| 33. Max Stassi | New York Yankees | 123. Anthont Varvaro | Arizona Diamondbacks |
| 34. Seth Maness | Boston Red Sox | 124. Carlos Torres | Boston Red Sox |
| 35. Kevin Siegrist | New York Yankees | 125. Chris Coghlan | San Diego Padres |
| 36. Ryan Goins | Pittsburgh Pirates | 126. Miguel Tejada | Miami Marlins |
| 37. Tyler Lyons | Colorado Rockies | 127. Vidal Nuno | Minnesota Twins |
| 38. Brandon Barnes | Cleveland Indians | 128. Joey Terdoslavich | New Your Mets |
| 39. Caleb Theilbar | Boston Red Sox | 129. Hector Rondon | Houston Astros |
| 40. Aaron Hicks | Atlanta Braves | 130. Michael Tonkin | Atlanta Braves |
| 41. Josh Phegley | Pittsburgh Pirates | 131. Todd Cunningham | Cleveland Indians |
| 42. Jose Ramirez | Los Angeles Angels | 132. Chen Chang Lee | Los Angeles Angels |
| 43. David Holmberg | Milwaukee Brewers | 133. Chris Rusin | Los Angeles Dodgers |
| 44. Tim Beckham | Colorado Rockies | 134. Wilfredo Tovar | Philadelphia Phillies |
| 45. Ed Lucas | Kansas City Royals | 135. Drake Britton | Boston Red Sox |
| 46. Stephen Vogt | Kansas City Royals | 136. Clete Thomas | Kansas City Royals |
| 47. Chris Withrow | Kansas City Royals | 137. Ehire Adrianza | St. Louis Cardinals |
| 48. Enny Ramero | Tampa Bay Rays | 138. Juan Perez | San Francisco Giants |
| 49. Brandon Workman | Toronto Blue Jays | 139. Will Harris | Chicago Cubs |
| 50. Wilmer Flores | Tampa Bay Rays | 140. Kyuji Fujikawa | Oakland A's |
| 51. Neal Cotts | Philadelphia Phillies | 141. Heath Bell | Tampa Bay Rays |
| 52. Caleb Gindl | Toronto Blue Jays | 142. Kyle Drabek | Toronto Blue Jays |
| 53. Marcus Semien | Cincinnati Reds | 143. Brian Flynn | Chicago White Sox |
| 54. Tanner Roark | Minnesota Twins | 144. Andrew Albers | Minnesota Twins |
| 55. Derek Dietrich | Oakland A's | 145. Tuffy Gosewisch | Cincinnati Reds |
| 56. Grant Green | Los Angeles Angels | 146. Dan Otero | Arizona Diamondbacks |
| 57. Josh Fields | Houston Astros | 147. Kevin Pillar | Milwaukee Brewers |
| 58. Alex Colome | Chicago Cubs | 148. Roger Kieschnick | San Francisco Giants |
| 59. Jeff Baker | Seattle Mariners | 149. Zeke Spruill | Arizona Diamondbacks |
| 60. Johnny Hellweg | Houston Astros | 150. Onelki Garcia | St. Louis Cardinals |
| 3rd Round | |||
| 61. Matt den Dekker | New York Mets | ||
| 62. Danny Valencia | Detroit Tigers | ||
| 63. Cesar Hernandez | Pittsburgh Pirates | ||
| 64. Taylor Jordan | Los Angeles Dodgers | ||
| 65. Reymond Fuentes | New York Yankees | ||
| 66. Ryan Pressly | New York Yankees | ||
| 67. Mike Dunn | Colorado Rockies | ||
| 68. Alfredo Simon | Philadelphia Phillies | ||
| 69. Brandon Cumpton | Colorado Rockies | ||
| 70. Zach Walters | Minnesota Twins | ||
| 71. John Gast | Cleveland Indians | ||
| 72. Dane De La Rosa | Los Angeles Angels | ||
| 73. Jonathan Pettibone | Arizona Diamondbacks | ||
| 74. Jeff Bianchi | Colorado Rockies | ||
| 75. Abraham Almonte | Houston Astros | ||
| 76. Anthony Recker | Kansas City Royals | ||
| 77. Nate Freiman | Tampa Bay Rays | ||
| 78. Josh Satin | Seattle Mariners | ||
| 79. Kevin Kirmaier | Chicago White Sox | ||
| 80. Henry Urruttia | Philadelphia Phillies | ||
| 81. Andrew Lambo | Chicago White Sox | ||
| 82. Tim Stauffer | Toronto Blue Jays | ||
| 83. Derrick Robinson | San Fransico Giants | ||
| 84. Burch Smith | San Diego Padres | ||
| 85. Blake Parker | Toronto Blue Jays | ||
| 86. Yoervis Medina | Baltimore Orioles | ||
| 87. Chris Colabello | Los Angeles Dodgers | ||
| 88. J.R. Murphy | Los Angeles Angels | ||
| 89. Tony Sanchez | Seattle Mariners | ||
| 90. Luis Jimenez | St. Louis Cardinals |