Players from NAIA schools taken in the 2021 Major League Baseball draft:
| Position | Player | School | Round | Overall | MLB team | Story |
| RHP | Garrett Hawkins | British Columbia | 9 | 280 | Padres | story |
| RHP | Malik Binns | Benedictine-Mesa | 18 | 535 | Phillies | |
| C | Kenny Piper | Columbia C. | 18 | 551 | Rays |