There were 160 players selected in the five rounds of the 2020 MLB Draft and 104 were from NCAA Division I programs, 65% of the total.
There were 65 different schools that had at least one player selected, led by Arizona State with five. Michigan, Oklahoma and Vanderbilt each had four, while Louisville, Miami, Mississippi State, Tennessee and Texas A&M each had three.
| Rd. | Pick | Team | Player | School | Pos. |
| 1 | 1 | Detroit | Spencer Torkelson | Arizona State | 3B |
| 1 | 2 | Baltimore | Heston Kjerstad | Arkansas | OF |
| 1 | 3 | Miami | Max Meyer | Minnesota | RHP |
| 1 | 4 | Kansas City | Asa Lacy | Texas A&M | LHP |
| 1 | 5 | Toronto | Austin Martin | Vanderbilt | SS |
| 1 | 6 | Seattle | Emerson Hancock | Georgia | RHP |
| 1 | 7 | Pittsburgh | Nick Gonzales | New Mexico State | SS |
| 1 | 10 | LA Angels | Reid Detmers | Louisville | LHP |
| 1 | 11 | Chicago WS | Garrett Crochet | Tennessee | LHP |
| 1 | 13 | San Francisco | Patrick Bailey | NC State | C |
| 1 | 14 | Texas | Justin Foscue | Mississippi State | 2B |
| 1 | 18 | Arizona | Bryce Jarvis | Duke | RHP |
| 1 | 20 | Milwaukee | Garrett Mitchell | UCLA | OF |
| 1 | 22 | Washington | Cade Cavalli | Oklahoma | RHP |
| 1 | 25 | Atlanta | Jared Shuster | Wake Forest | LHP |
| 1 | 27 | Minnesota | Aaron Sabato | North Carolina | 1B |
| 1 | 28 | NY Yankees | Austin Wells | Arizona | C |
| 1 | 29 | LA Dodgers | Bobby Miller | Louisville | RHP |
| CBA | 30 | Baltimore | Jordan Westburg | Mississippi State | SS |
| CBA | 31 | Pittsburgh | Carmen Mlodzinski | South Carolina | RHP |
| CBA | 32 | Kansas City | Nick Loftin | Baylor | SS |
| CBA | 33 | Arizona | Slade Cecconi | Miami | RHP |
| CBA | 36 | Cleveland | Tanner Burns | Auburn | RHP |
| CBA | 37 | Tampa Bay | Alika Williams | Arizona State | SS |
| 2 | 38 | Detroit | Dillon Dingler | Ohio State | C |
| 2 | 39 | Baltimore | Hudson Haskin | Tulane | OF |
| 2 | 42 | Toronto | CJ Van Eyk | Florida State | RHP |
| 2 | 43 | Seattle | Zach DeLoach | Texas A&M | OF |
| 2 | 46 | Colorado | Chris McMahon | Miami | RHP |
| 2 | 48 | Cincinnati | Christian Roa | Texas A&M | RHP |
| 2 | 49 | San Francisco | Casey Schmitt | San Diego State | 3B |
| 2 | 51 | Chicago Cubs | Burl Carraway | Dallas Baptist | LHP |
| 2 | 52 | NY Mets | J.T. Ginn | Mississippi State | RHP |
| 2 | 53 | Milwaukee | Freddy Zamora | Miami | SS |
| 2 | 55 | Washington | Cole Henry | LSU | RHP |
| 2 | 56 | Cleveland | Logan Allen | FIU | LHP |
| 2 | 57 | Tampa Bay | Ian Seymour | Virginia Tech | LHP |
| 2 | 58 | Oakland | Jeff Criswell | Michigan | RHP |
| 2 | 59 | Minnesota | Alerick Soularie | Tennessee | OF |
| 2 | 60 | LA Dodgers | Landon Knack | East Tennessee St. | RHP |
| CBB | 61 | Miami | Kyle Nicolas | Ball State | RHP |
| CBB | 62 | Detroit | Danny Cabrera | LSU | OF |
| CBB | 66 | LA Dodgers | Clayton Beeter | Texas Tech | RHP |
| 2C | 67 | San Francisco | Nick Swiney | NC State | LHP |
| 2C | 68 | San Francisco | Jimmy Glowenke | Dallas Baptist | SS |
| 2C | 70 | St. Louis | Alec Burleson | East Carolina | OF |
| 3 | 73 | Detroit | Trei Cruz | Rice | SS |
| 3 | 74 | Baltimore | Anthony Servideo | Ole Miss | SS |
| 3 | 75 | Miami | Zach McCambley | Coastal Carolina | RHP |
| 3 | 76 | Kansas City | Tyler Gentry | Alabama | OF |
| 3 | 77 | Toronto | Trent Palmer | Jacksonville | RHP |
| 3 | 78 | Seattle | Kaden Polcovich | Oklahoma State | 2B |
| 3 | 80 | San Diego | Cole Wilcox | Georgia | RHP |
| 3 | 81 | Colorado | Sam Weatherly | Clemson | LHP |
| 3 | 84 | Cincinnati | Bryce Bonnin | Texas Tech | RHP |
| 3 | 87 | Philadelphia | Casey Martin | Arkansas | SS |
| 3 | 88 | Chicago Cubs | Jordan Nwogu | Michigan | OF |
| 3 | 91 | NY Mets | Anthony Walters | San Diego State | SS |
| 3 | 92 | Milwaukee | Zavier Warren | Central Michigan | C |
| 3 | 93 | St. Louis | Levi Prater | Oklahoma | LHP |
| 3 | 94 | Washington | Holden Powell | UCLA | RHP |
| 3 | 97 | Atlanta | Jesse Franlkin | Michigan | LHP |
| 3 | 98 | Oakland | Michael Guldberg | Georgia Tech | OF |
| 3 | 99 | NY Yankees | Trevor Hauver | Arizona State | 2B |
| 3 | 101 | Houston | Ty Brown | Vanderbilt | RHP |
| 4 | 102 | Detroit | Gage Workman | Arizona State | 3B |
| 4 | 104 | Miami | Jake Eder | Vanderbilt | LHP |
| 4 | 105 | Kansas City | Christian Chamberlain | Oregon State | LHP |
| 4 | 106 | Toronto | Nick Frasso | Loyola Marymount | RHP |
| 4 | 107 | Seattle | Tyler Keenan | Ole Miss | 3B |
| 4 | 108 | Pittsburgh | Jack Hartman | Appalachian State | RHP |
| 4 | 109 | San Diego | Levi Thomas | Troy | RHP |
| 4 | 112 | Chicago WS | Kade Mechals | Grand Canyon | RHP |
| 4 | 114 | San Francisco | R.J. Dabovich | Arizona State | RHP |
| 4 | 116 | Philadelphia | Carson Ragsdale | South Florida | RHP |
| 4 | 118 | Boston | Jeremy Wu-Yelland | Hawaii | LHP |
| 4 | 120 | NY Mets | Matthew Dyer | Arizona | C |
| 4 | 121 | Milwaukee | Joey Wiemer | Cincinnati | OF |
| 4 | 122 | St. Louis | Ian Bedell | Missouri | RHP |
| 4 | 123 | Washington | Brady Lindsly | Oklahoma | C |
| 4 | 125 | Tampa Bay | Tanner Murray | UC Davis | SS |
| 4 | 126 | Atlanta | Spencer Strider | Clemson | RHP |
| 4 | 127 | Oakland | Dane Acker | Oklahoma | RHP |
| 4 | 130 | LA Dodgers | Carson Taylor | Virginia Tech | C |
| 4 | 131 | Houston | Zach Daniels | Tennessee | OF |
| 5 | 134 | Miami | Kyle Hurt | USC | RHP |
| 5 | 135 | Kansas City | Will Klein | Eastern Illinois | RHP |
| 5 | 136 | Toronto | Zach Britton | Louisville | OF |
| 5 | 137 | Seattle | Taylor Dollard | Cal Poly | RHP |
| 5 | 138 | Pittsburgh | Logan Hofmann | Northwestern State | RHP |
| 5 | 140 | Colorado | Jack Blomgren | Michigan | SS |
| 5 | 141 | LA Angels | Adam Seminaris | Long Beach State | LHP |
| 5 | 142 | Chicago WS | Bailey Horn | Auburn | LHP |
| 5 | 143 | Cincinnati | Joe Boyle | Notre Dame | RHP |
| 5 | 146 | Philadelphia | Baron Radcliff | Georgia Tech | OF |
| 5 | 148 | Boston | Shane Drohan | Florida State | LHP |
| 5 | 150 | NY Mets | Eric Orze | New Orleans | RHP |
| 5 | 151 | Milwaukee | Hayden Cantrelle | UL Lafayette | SS |
| 5 | 152 | St. Louis | Leonard Jones | Long Beach State | OF |
| 5 | 154 | Cleveland | Mason Hickman | Vanderbilt | RHP |
| 5 | 155 | Tampa Bay | Jeff Hakanson | Central Florida | RHP |
| 5 | 156 | Atlanta | Bryce Elder | Texas | RHP |
| 5 | 157 | Oakland | Stevie Emanuels | Washington | RHP |
| 5 | 159 | LA Dodgers | Gavin Stone | Central Arkansas | RHP |