Baseball America has released its 2020 edition of the Top 30 prospects in the Toronto Blue Jays system.

2019 fifth-round pick Tanner Morris made it onto Baseball America's Top 30 Jays prospects list.
| No.# | Player | Position |
| 1 | Nate Pearson | RHP |
| 2 | Jordan Groshans | SS |
| 3 | Simeon Woods-Richardson | RHP |
| 4 | Alejandro Kirk | C |
| 5 | Alek Manoah | RHP |
| 6 | Orelvis Martinez | 3B |
| 7 | Gabriel Moreno | C |
| 8 | Miguel Hiraldo | SS |
| 9 | Anthony Kay | LHP |
| 10 | Adam Kloffenstein | RHP |
| 11 | Otto Lopez | SS/2B |
| 12 | Estiven Machado | SS |
| 13 | Shun Yamaguchi | RHP |
| 14 | Kendall Williams | RHP |
| 15 | Eric Pardinho | RHP |
| 16 | Griffin Conine | OF |
| 17 | Leonardo Jimenez | SS |
| 18 | Rikelvin de Castro | SS |
| 19 | Patrick Murphy | RHP |
| 20 | Victor Mesia | C |
| 21 | Santiago Espinal | SS/2B |
| 22 | Alberto Rodriguez | OF |
| 23 | Dasan Brown | OF |
| 24 | Reese McGuire | C |
| 25 | Anthony Alford | OF |
| 26 | Kevin Smith | SS |
| 27 | Joey Murray | RHP |
| 28 | Yennsy Diaz | RHP |
| 29 | Tanner Morris | SS |
| 30 | Will Robertson | OF |
Breakout Prospect - Estiven Machado, SS
Sleeper Prospect - Dahian Santos, RHP
Top Rookie - Nate Pearson, RHP
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