Players from NAIA schools taken in the 2016 Major League Baseball draft:
| Pick | Round | Team | Player | Story | School | Pos. |
| 46 | 2 | Milwaukee Brewers | Lucas Erceg | story | Menlo (Calif.) | 3B |
| 119 | 4 | Arizona Diamondbacks | Curtis Taylor | story | British Columbia | RHP |
| 209 | 7 | Arizona Diamondbacks | Jordan Watson | Science & Arts (Okla.) | LHP | |
| 234 | 8 | San Diego Padres | Benjamin Sheckler | story | Cornerstone (Mich.) | LHP |
| 258 | 9 | Cincinnati Reds | Alex Webb | British Columbia | RHP | |
| 266 | 9 | Chicago White Sox | Max Dutto | Menlo (Calif.) | SS | |
| 277 | 9 | Houston Astros | Ryan Hartman | story | Tennessee Wesleyan | LHP |
| 309 | 10 | Texas Rangers | Josh Merrigan | story | Georgia Gwinnett | OF |
| 379 | 13 | Atlanta Braves | Brandon White | story | Davenport (Mich.) | RHP |
| 416 | 14 | Chicago White Sox | Bryan Saucedo | story | Davenport (Mich.) | RHP |
| 425 | 14 | San Francisco Giants | Conner Menez | story | The Master's (Calif.) | LHP |
| 445 | 15 | Detroit Tigers | John Schreiber | story | Northwestern Ohio | RHP |
| 464 | 15 | Chicago Cubs | Jed Carter | story | Auburn Montgomery (Ala.) | RHP |
| 474 | 16 | San Diego Padres | Chris Mattison | story | Southeastern (Fla.) | C |
| 480 | 16 | New York Mets | Jacob Zanon | story | Lewis-Clarke State (Idaho) | CF |
| 575 | 19 | San Francisco Giants | Brandon Van Horn | The Master's (Calif.) | SS | |
| 604 | 20 | Washington Nationals | Jake Barnett | Lewis-Clarke State (Idaho) | LHP | |
| 694 | 23 | Washington Nationals | Michael Rishwain | story | Westmont (Calif.) | RHP |
| 708 | 24 | Cincinnati Reds | Bruce Yari | story | British Columbia | 1B |
| 744 | 25 | San Diego Padres | Luis Anguizola | Loyola (La.) | C | |
| 778 | 26 | Boston Red Sox | Jared Oliver | Truett-McConnell | RHP | |
| 799 | 27 | Atlanta Braves | Corbin Clouse | Davenport (Mich.) | LHP | |
| 801 | 27 | Milwaukee Brewers | Nick Cain | Faulkner (Ala.) | RF | |
| 860 | 29 | Colorado Rockies | Josh Shelley | Mobile (Ala.) | RHP | |
| 886 | 29 | St. Louis Cardinals | Noel Gonzalez | Lewis-Clarke State (Idaho) | RHP | |
| 903 | 30 | Minnesota Twins | Quin Grogan | Lewis-Clarke State (Idaho) | RHP | |
| 909 | 30 | Texas Rangers | Christian Torres | Faulkner (Ala.) | LHP | |
| 922 | 31 | Oakland Athletics | Sam Sheehan | Westmont (Calif.) | RHP | |
| 953 | 32 | Miami Marlins | Chevis Hoover | Tennessee Wesleyan | RHP | |
| 965 | 32 | San Francisco Giants | John Timmins | Bellevue (Neb.) | RHP | |
| 969 | 32 | Texas Rangers | Travis Bolin | Davenport (Mich.) | OF | |
| 976 | 32 | St. Louis Cardinals | Leland Tilley | Bellevue (Neb.) | RHP | |
| 982 | 33 | Oakland Athletics | Jarrett Costa | Westmont (Calif.) | C | |
| 999 | 33 | Texas Rangers | Mark Vasquez | Faulkner (Ala.) | RHP | |
| 1056 | 35 | Los Angeles Angels | Sean Issac | Vanguard (Calif.) | RHP | |
| 1086 | 36 | Los Angeles Angels | Jose Rojas | Vanguard (Calif.) | SS | |
| 1121 | 37 | Los Angeles Dodgers | Enrique Zamora | Calument (Ind.) | RHP | |
| 1134 | 38 | San Diego Padres | Will Solomon | Georgia Gwinnett | LHP | |
| 1161 | 39 | Milwaukee Brewers | Jose Gomez | St. Thomas (Fla.) | CF |