Players from NAIA schools taken in the 2019 Major League Baseball draft:
| Position | Player | School | Round | Overall | MLB team | Story |
| 2B | Cam Coursey | Georgia Gwinnett | 13 | 392 | Diamondbacks | story |
| SS | Aaron Shackelford | The Master's | 14 | 424 | Pirates | story |
| RHP | Shaine McNeely | Hope International | 16 | 496 | Yankees | |
| LHP | Niall Windeler | British Columbia | 19 | 569 | Twins | story |
| RHP | Bryce Milligan | Oklahoma City | 19 | 593 | Brewers | |
| RHP | Eddie Tavarez | Peru State | 21 | 643 | Brewers | story |
| RHP | Matthew Swain | Georgia Gwinnett | 23 | 689 | Twins | |
| RHP | Justin Friedman | Hope International | 26 | 770 | White Sox | |
| C | Anthony Lepre | The Master's | 28 | 846 | Mariners | |
| CF | Elliott Cary | Oklahoma City | 29 | 862 | Tigers | |
| 2B | Jackie Urbaez | Saint Thomas | 29 | 883 | Brewers | |
| RHP | Peyton Long | Central Methodist | 30 | 913 | Brewers | story |
| C | Dylan Shockley | Rio Grande | 34 | 1,024 | Pirates | |
| LF | Willie Carter | Webber International | 34 | 1,027 | Braves | |
| LHP | Dylan Hoffman | Waldorf | 39 | 1,163 | Padres |