Out of the first 90 players selected in the 2025 Major League Draft, 63% were NCAA Division I players.
There were 34 college players taken among the 60 first-round picks and 57 of 90 in the first two round.
There were 36 schools to have players chosen in the first two rounds and 10 programs with multiple picks. Tennessee led the way with seven selections. Arkansas and Florida State had four, LSU and Oklahoma had three, while Arizona, North Carolina, Southern Miss, Texas A&M and Wake Forest had two each.
| Rd. | Pick | Team | Player | School | Pos. |
| 1 | 2 | LA Angels | Tyler Bremner | UCSB | RHP |
| 1 | 3 | Seattle | Kade Anderson | LSU | LHP |
| 1 | 5 | St. Louis | Liam Doyle | Tennessee | LHP |
| 1 | 7 | Miami | Aiva Arquette | Oregon State | SS |
| 1 | 11 | Athletics | Jamie Arnold | Florida State | LHP |
| 1 | 13 | San Francisco | Gavin Kilen | Tennessee | SS |
| 1 | 15 | Boston | Kyson Witherspoon | Oklahoma | RHP |
| 1 | 16 | Minnesota | Marek Houston | Wake Forest | SS |
| 1 | 17 | Chicago Cubs | Ethan Conrad | Wake Forest | OF |
| 1 | 19 | Baltimore | Ike Irish | Auburn | C |
| 1 | 20 | Milwaukee | Andrew Fischer | Tennessee | 3B |
| 1 | 26 | Philadelphia | Gage Wood | Arkansas | RHP |
| 1 | 27 | Cleveland | Jace LaViolette | Texas A&M | OF |
| 1 | 29 | Arizona | Patrick Forbes | Louisville | RHP |
| 1 | 30 | Baltimore | Caden Bodine | Coastal Carolina | C |
| 1 | 31 | Baltimore | Wehiwa Aloy | Arkansas | SS |
| 1 | 33 | Boston | Marcus Phillips | Tennessee | RHP |
| 1 | 35 | Seattle | Luke Stevenson | North Carolina | C |
| 1 | 36 | Minnesota | Riley Quick | Alabama | RHP |
| 1 | 38 | NY Mets | Mitch Voit | Michigan | TWP |
| 1 | 40 | LA Dodgers | Zach Root | Arkansas | LHP |
| 1 | 41 | LA Dodgers | Charles Davalan | Arkansas | OF |
| 1 | 42 | Tampa Bay | Brendan Summerhill | Arizona | OF |
| 1 | 43 | Miami | Cam Cannarella | Clemson | OF |
| 1 | 45 | Colorado | JB Middleton | Southern Miss | RHP |
| 1 | 46 | Miami | Brandon Compton | Arizona State | OF |
| 1 | 47 | LA Angels | Chase Shores | LSU | RHP |
| 1 | 48 | Athletics | Devin Taylor | Indiana | OF |
| 1 | 49 | Washington | Ethan Petry | South Carolina | OF |
| 1 | 52 | Texas | AJ Russell | Tennessee | RHP |
| 1 | 56 | Chicago Cubs | Kane Kepley | North Carolina | OF |
| 1 | 58 | Baltimore | Joseph Dzierwa | Michigan State | LHP |
| 1 | 59 | Milwaukee | J.D. Thompson | Vanderbilt | LHP |
| 1 | 60 | Atlanta | Alex Lodise | Florida State | SS |
| 2 | 61 | Kansas City | Michael Lombardi | Tulane | RHP |
| 2 | 62 | Detroit | Malachi Witherspoon | Oklahoma | RHP |
| 2 | 63 | Philadelphia | Cade Obermueller | Iowa | LHP |
| 2 | 64 | Cleveland | Dean Curley | Tennessee | SS |
| 2 | 65 | LA Dodgers | Cam Leiter | Florida State | RHP |
| 2 | 66 | Cleveland | Aaron Walton | Arizona | OF |
| 2 | 69 | Baltimore | JT Quinn | Georgia | RHP |
| 2 | 71 | Kansas City | Justin Lamkin | Texas A&M | LHP |
| 2 | 72 | St. Louis | Tanner Franklin | Tennessee | RHP |
| 2 | 73 | Pittsburgh | Murf Gray | Fresno State | 3B |
| 2 | 74 | Colorado | Max Belyeu | Texas | OF |
| 2 | 75 | Boston | Henry Godbout | Virginia | SS |
| 2 | 76 | Chicago WS | Kyle Lodise | Georgia Tech | SS |
| 2 | 77 | Colorado | Ethan Hedges | USC | 3B |
| 2 | 78 | Miami | Max Williams | Florida State | OF |
| 2 | 81 | Toronto | Jake Cook | Southern Miss | OF |
| 2 | 82 | Pittsburgh | Easton Carmichael | Oklahoma | C |
| 2 | 83 | Cincinnati | Mason Morris | Ole Miss | RHP |
| 2 | 85 | San Francisco | Trevor Cohen | Rutgers | OF |
| 2 | 87 | Boston | Anthony Eyanson | LSU | RHP |
| 2 | 88 | Minnesota | James Ellwanger | Dallas Baptist | RHP |
| 2 | 89 | St. Louis | Jack Gurevitch | San Diego | 1B |
| 2 | 90 | Chicago Cubs | Dominick Reid | Abilene Christian | RHP |