On Day 3 of the 2021 MLB Draft, the Marlins selected the following players:
- Round 11, No. 329 overall pick—Jesse Bergin, RHP, UCLA
- Round 12, No. 359 overall pick—Brandon White, RHP, Washington State
- Round 13, No. 389 overall pick—Chandler Jozwiak, LHP, Texas A&M
- Round 14, No. 419 overall pick—Holt Jones Jr., RHP, Kentucky
- Round 15, No. 449 overall pick—Caleb Wurster, LHP, Connecticut
- Round 16, No. 479 overall pick—Ivan Melendez, INF, Texas
- Round 17, No.