Players from NAIA schools taken in the 2018 Major league Baseball draft:
| Position | Player | School | Round | Overall | MLB team | Story |
| C | Elih Marrero | Saint Thomas | 8 | 250 | Red Sox | story |
| RHS | Ben Madison | Central Baptist | 9 | 256 | Giants | story |
| RHS | Alex DuBord | Faulkner | 10 | 286 | Giants | story |
| RHS | Shawn Dubin | Georgetown C. | 13 | 402 | Astros | story |
| RF | Marvin Malone | Southeastern | 16 | 480 | Rays | story |
| C | Lane Milligan | Oklahoma City | 17 | 520 | Red Sox | story |
| RHR | Eddie Jimenez | Southeastern | 18 | 550 | Red Sox | |
| RHR | Angel Reyes | Science and Arts of Oklahoma | 19 | 555 | Tigers | story |
| RHS | Stephen Yancey | Texas Wesleyan | 20 | 600 | Rays | |
| 3B | Mitch Robinson | British Columbia | 21 | 637 | Yankees | story |
| RHP | Gage Burland | Lewis-Clark State | 22 | 656 | Blue Jays | story |
| LHP | Jonathan Bermudez | Southeastern | 23 | 702 | Astros | |
| OF | Preston White | The Master's | 24 | 706 | Giants | story |
| C | Rusber Estrada | Faulkner | 24 | 712 | Braves | |
| RHP | Miguel Figueroa | Oklahoma City | 24 | 732 | Astros | |
| RHS | Kris Jackson | Corban | 28 | 850 | Red Sox | story |
| C | Nelson Mompierre | Saint Thomas | 29 | 860 | Mets | |
| LHP | Andrew Shaps | William Jessup | 31 | 944 | Dodgers | story |
| 3B | Joe Gillette | Menlo | 36 | 1089 | Diamondbacks | |
| LF | Matthew Jarecki | Benedictine (KS) | 37 | 1095 | Tigers | |
| RHR | Alex Camacho | Vanguard | 37 | 1102 | Braves | |
| RHS | Bobby Milacki | Arizona Christian | 38 | 1151 | Nationals | |
| C | Kevynn Arias | Montreat | 40 | 1185 | Tigers | |
| RHS | Brian Metoyer | LSU-Alexandria | 40 | 1190 | Mets | |
| RHP | Cole Uvila | Georgia Gwinnett | 40 | 1199 | Rangers | |
| RF | Andrew Warner | Columbia C. | 40 | 1203 | Cardinals |