| Game Date |
| Opponent | Conference Game | Result | Commentary |
| 2/20/2009 | at | Florida International |
| L 4-3 |
|
| 2/21/2009 | at | Florida International |
| L 20-1 |
|
| 2/22/2009 | at | Florida International |
| W 9-3 |
|
| 2/27/2009 |
| Akron |
| W 6-4 | Jacksonville Invitational, Jacksonville, FL |
| 2/28/2009 |
| Michigan |
| L 21-3 | Jacksonville Invitational, Jacksonville, FL |
| 2/28/2009 |
| Michigan |
| W 10-2 | Jacksonville Invitational, Jacksonville, FL |
| 3/1/2009 |
| Wisconsin-Milwaukee |
| L 10-9 | 7 innings (Jacksonville Invitational, Jacksonville, FL) |
| 3/3/2009 |
| Florida State |
| W 9-4 |
|
| 3/4/2009 |
| Florida A&M |
|
| PPD to 3/11, scheduling conflict |
| 3/6/2009 |
| North Florida | * | L 4-2 |
|
| 3/7/2009 |
| North Florida | * | W 4-3 |
|
| 3/8/2009 |
| North Florida | * | W 8-7 | 600th career win for JU's Terry Alexander |
| 3/10/2009 |
| Georgia Southern |
| W 8-7 |
|
| 3/11/2009 |
| Florida A&M |
| W 9-4 | makeup of 3/4 game |
| 3/13/2009 |
| Stetson | * | L 9-6 |
|
| 3/14/2009 |
| Stetson | * | L 22-8 |
|
| 3/15/2009 |
| Stetson | * | W 18-8 |
|
| 3/18/2009 | at | Bethune-Cookman |
| W 9-6 |
|
| 3/20/2009 | at | Florida Gulf Coast | * | W 3-2 |
|
| 3/21/2009 | at | Florida Gulf Coast | * | W 7-2 |
|
| 3/22/2009 | at | Florida Gulf Coast | * | L 5-4 |
|
| 3/24/2009 | at | UCF |
| W 14-9 |
|
| 3/25/2009 |
| UCF |
| W 9-5 |
|
| 3/27/2009 |
| South Carolina-Upstate | * | W 4-3 |
|
| 3/28/2009 |
| South Carolina-Upstate | * | W 14-1 | 7 innings |
| 3/28/2009 |
| South Carolina-Upstate | * | W 14-7 |
|
| 3/31/2009 |
| Florida International |
| W 9-7 | 8 innings, rain |
| 4/1/2009 |
| Florida International |
|
| CCD, inclement weather |
| 4/3/2009 | at | Belmont | * | W 3-1 |
|
| 4/4/2009 | at | Belmont | * | L 12-7 |
|
| 4/4/2009 | at | Belmont | * | L 15-10 | moved from 4/5 |
| 4/7/2009 |
| South Florida |
| W 12-10 |
|
| 4/8/2009 |
| South Florida |
|
| PPD, travel conflict |
| 4/9/2009 | at | East Tennessee State | * | W 17-10 |
|
| 4/10/2009 | at | East Tennessee State | * |
| Suspended to 4/11, rain (2-0 ETSU, top 2) |
| 4/11/2009 | at | East Tennessee State | * | W 12-10 | Resumption of 4/10 game |
| 4/11/2009 | at | East Tennessee State | * | W 4-3 |
|
| 4/15/2009 | at | Georgia Southern |
| L 4-2 |
|
| 4/17/2009 |
| Campbell | * | L 3-2 |
|
| 4/18/2009 |
| Campbell | * | W 7-6 |
|
| 4/18/2009 |
| Campbell | * | W 10-5 |
|
| 4/24/2009 |
| Lipscomb | * | W 7-6 |
|
| 4/25/2009 |
| Lipscomb | * | W 12-2 |
|
| 4/26/2009 |
| Lipscomb | * | L 3-2 |
|
| 4/29/2009 |
| Bethune-Cookman |
| W 3-2 | 10 innings |
| 5/1/2009 | at | Kennesaw State | * |
| Suspended to 5/2, inclement weather (1-1, top 11) |
| 5/2/2009 | at | Kennesaw State | * | W 2-1 | 15 innings (Resumption of 5/1 game) |
| 5/2/2009 | at | Kennesaw State | * | L 11-4 |
|
| 5/2/2009 | at | Kennesaw State | * |
| PPD to 5/3, scheduling |
| 5/3/2009 | at | Kennesaw State | * | L 15-9 | makeup of 5/2 game |
| 5/4/2009 | at | Florida A&M |
| W 11-3 |
|
| 5/5/2009 | at | Florida State |
| L 5-2 |
|
| 5/6/2009 |
| Bethune-Cookman |
| W 12-4 | 5 innings, inclement weather |
| 5/9/2009 | at | Mercer | * | L 6-1 |
|
| 5/10/2009 | at | Mercer | * | W 11-10 |
|
| 5/11/2009 | at | Mercer | * | W 23-5 |
|
| 5/12/2009 | at | Florida |
| L 7-4 |
|
| 5/14/2009 |
| Dallas Baptist |
| L 13-1 |
|
| 5/15/2009 |
| Dallas Baptist |
| L 7-2 |
|
| 5/16/2009 |
| Dallas Baptist |
| W 13-3 |
|
| 5/20/2009 | vs | East Tennessee State | ATLSUN-01 |
| Atlantic Sun Tournament, Game 1 (DeLand, FL) PPD to 5/21, rain |
| 5/23/2009 | vs | Belmont | ATLSUN-03 | W 7-5 | Atlantic Sun Tournament, Game 3 (DeLand, FL) |
| 5/23/2009 | vs | Lipscomb | ATLSUN-05 |
| Atlantic Sun Tournament, Game 5 (DeLand, FL) Suspended to 5/24, rain (1-0 Lipscomb, t2) |
| 5/24/2009 | vs | Lipscomb | ATLSUN-05 | W 7-4 | Atlantic Sun Tournament, Game 5 (DeLand, FL) Resumption |
| 5/29/2009 | vs | Miami, Florida |
| L 9-4 | Gainesville Regional, Game 1 |
| 5/30/2009 | vs | Bethune-Cookman |
| W 8-7 | Gainesville Regional, Game 3 |
| 5/31/2009 | vs | Miami, Florida |
| L 4-0 | Gainesville Regional, Game 5 |
| Game Date |
| Opponent | Conference Game | Result | Commentary |
| 2/20/2009 | vs | Northern Illinois |
| W 6-3 | BankFirst Baseball Challenge, Starkville, MS |
| 2/21/2009 | at | Mississippi State |
| L 7-1 | BankFirst Baseball Challenge, Starkville, MS |
| 2/22/2009 | vs | Northern Illinois |
| W 9-3 | BankFirst Baseball Challenge, Starkville, MS |
| 2/22/2009 | at | Mississippi State |
| L 9-7 | BankFirst Baseball Challenge, Starkville, MS |
| 2/25/2009 |
| Michigan |
| L 9-8 |
|
| 2/27/2009 |
| Ohio State |
| L 11-6 | Kennel Club Classic, Jacksonville, FL |
| 2/28/2009 |
| Connecticut |
| L 10-2 | Kennel Club Classic, Jacksonville, FL |
| 2/28/2009 |
| Ohio State |
| L 10-8 | Kennel Club Classic, Jacksonville, FL |
| 3/1/2009 |
| George Mason |
| W 15-11 | Kennel Club Classic, Jacksonville, FL |
| 3/4/2009 | at | Florida State |
| W 5-4 |
|
| 3/6/2009 | at | Jacksonville | * | W 4-2 |
|
| 3/7/2009 | at | Jacksonville | * | L 4-3 |
|
| 3/8/2009 | at | Jacksonville | * | L 8-7 | 600th career win for JU's Terry Alexander |
| 3/10/2009 |
| Troy |
| L 8-7 |
|
| 3/11/2009 |
| Troy |
| W 10-9 | 12 innings |
| 3/14/2009 |
| Florida Gulf Coast | * | L 6-0 |
|
| 3/14/2009 |
| Florida Gulf Coast | * | L 8-2 |
|
| 3/15/2009 |
| Florida Gulf Coast | * | L 8-2 |
|
| 3/17/2009 | at | Florida International |
| L 10-6 |
|
| 3/18/2009 | at | Florida International |
| L 3-0 |
|
| 3/20/2009 |
| Belmont | * | L 8-5 |
|
| 3/21/2009 |
| Belmont | * | W 3-0 |
|
| 3/21/2009 |
| Belmont | * | W 11-5 |
|
| 3/24/2009 |
| Florida |
| W 3-0 |
|
| 3/25/2009 | at | Florida |
| L 5-3 |
|
| 3/27/2009 | at | Campbell | * | W 13-3 | 6 innings, rain |
| 3/28/2009 | at | Campbell | * |
| PPD to 3/30, inclement weather |
| 3/28/2009 | at | Campbell | * |
| PPD to 3/30, inclement weather |
| 3/30/2009 | at | Campbell | * | W 12-2 | makeup of 3/28 game |
| 3/30/2009 | at | Campbell | * | W 16-13 | makeup of 3/28 game |
| 3/31/2009 | at | Georgia Southern |
|
| PPD, rain and lightning |
| 4/1/2009 | at | UCF |
| L 8-2 |
|
| 4/4/2009 |
| East Tennessee State | * | W 15-3 | 7 innings |
| 4/4/2009 |
| East Tennessee State | * | W 8-6 |
|
| 4/5/2009 |
| East Tennessee State | * | L 12-8 |
|
| 4/7/2009 |
| UCF |
| L 7-3 |
|
| 4/8/2009 |
| Florida State |
| L 14-6 |
|
| 4/10/2009 | at | Lipscomb | * | W 1-0 |
|
| 4/11/2009 | at | Lipscomb | * | L 6-3 |
|
| 4/11/2009 | at | Lipscomb | * | L 11-4 |
|
| 4/14/2009 |
| Georgia Southern |
|
| PPD, inclement weather |
| 4/15/2009 | at | Florida State |
| L 8-7 |
|
| 4/25/2009 |
| Mercer | * | W 10-0 | 7 innings |
| 4/25/2009 |
| Mercer | * | W 8-6 |
|
| 4/26/2009 |
| Mercer | * | L 7-2 |
|
| 4/28/2009 | at | Miami, Florida |
| W 10-1 |
|
| 5/1/2009 | at | Stetson | * | L 14-1 |
|
| 5/2/2009 | at | Stetson | * | W 11-9 | 10 innings |
| 5/3/2009 | at | Stetson | * | L 10-8 |
|
| 5/5/2009 | at | Bethune-Cookman |
| L 11-1 |
|
| 5/6/2009 |
| South Florida |
|
| Suspended to 5/12, inclement weather (7-6 UNF, bottom 5) |
| 5/9/2009 | at | South Carolina-Upstate | * | W 21-16 |
|
| 5/9/2009 | at | South Carolina-Upstate | * | L 8-7 |
|
| 5/10/2009 | at | South Carolina-Upstate | * | W 6-2 |
|
| 5/12/2009 | vs | South Florida |
| W 11-6 | Resumption of 5/6 game (Tampa, FL) |
| 5/12/2009 | at | South Florida |
| L 11-6 | 7 innings |
| 5/14/2009 |
| Kennesaw State | * | L 6-5 | 11 innings |
| 5/15/2009 |
| Kennesaw State | * | L 8-3 |
|
| 5/15/2009 |
| Kennesaw State | * | W 7-4 |
|