NOTE: Emory's first year of varsity competition in the NCAA was 1991.
| Year | W | L | T | UAA Finish |
W | L | NCAA Finish Region |
NCAA Finish Nation |
Final Rank Nation |
Coach |
| 1991 | 10 | 26 | 0 | - | 3 | 1 | - | - | - | Doug Kovash |
| 1992 | 23 | 21 | 0 | 2nd | 4 | 2 | - | - | - | Doug Kovash |
| 1993 | 27 | 14 | 0 | 3rd | 3 | 3 | - | - | - | Doug Kovash |
| 1994 | 29 | 13 | 0 | 1st (tie) | 5 | 1 | - | - | - | Kevin Howard |
| 1995 | 24 | 18 | 1 | 1st (tie) | 5 | 1 | - | - | - | Kevin Howard |
| 1996 | 29 | 16 | 0 | - | 2 | 3 | 4th | Round of 32 | 26 | Kevin Howard |
| 1997 | 32 | 16 | 0 | 3rd | 2 | 3 | 3rd | Round of 24 | 20 | Kevin Howard |
| 1998 | 33 | 16 | 0 | 3rd | 3 | 2 | 3rd | Round of 24 | 23 | Kevin Howard |
| 1999 | 30 | 13 | 0 | 1st | 4 | 1 | - | - | - | Kevin Howard |
| 2000 | 33 | 16 | 0 | 2nd | 6 | 1 | 1st | 7th | 7 | Mike Twardoski |
| 2001 | 36 | 9 | 0 | 1st | 6 | 1 | 2nd | Round of 16 | 9 | Mike Twardoski |
| 2002 | 26 | 16 | 0 | 2nd | 4 | 2 | - | - | - | Mike Twardoski |
| 2003 | 37 | 15 | 0 | 1st | 4 | 2 | 1st | 5th | 5 | Mike Twardoski |
| 2004 | 42 | 6 | 0 | 1st | 6 | 0 | 3rd | Round of 24 | 9 | Mike Twardoski |
| 2005 | 21 | 18 | 0 | 2nd | 3 | 3 | - | - | - | Mike Twardoski |
| 2006 | 31 | 9 | 0 | 1st | 6 | 0 | 6th | First Round | 30 | Mike Twardoski |
| 2007 | 43 | 10 | 0 | 1st | 4 | 2 | 1st | 2nd | 2 | Mike Twardoski |
| 2008 | 25 | 11 | 1 | t-1st | 4 | 2 | - | - | - | Mike Twardoski |
| 2009 | 24 | 18 | 0 | t-2nd | 3 | 3 | - | - | - | Mike Twardoski |
| 2010 | 19 | 20 | 0 | 3rd | 3 | 2 | - | - | - | Mike Twardoski |
| 2011 | 26 | 17 | 0 | 1st | 5 | 1 | - | - | - | Mike Twardoski |
| 2012 | 26 | 14 | 0 | 1st | 7 | 1 | 5th | NCAA Regionals | - | Mike Twardoski |
| 2013 | 22 | 17 | 0 | t-3rd | 4 | 4 | - | - | - | Mike Twardoski |
| 2014 | 38 | 13 | 0 | t-1st | 6 | 2 | 1st | 2nd | 3rd | Mike Twardoski |
| 2015 | 31 | 15 | 0 | t-1st | 6 | 2 | 1st | 5th | 7th | Mike Twardoski |
| 2016 | 34 | 12 | 0 | T-2nd | 5 | 3 | 1st | 7th | 5th | Mike Twardoski |
| 2017 | 27 | 14 | 0 | 3rd | 9 | 7 | 5th | NCAA Regionals | - | Mike Twardoski |
| 2018 | 20 | 18 | 0 | 2nd | 11 | 5 | - | - | - | Mike Twardoski |
| 2019 | 20 | 19 | 0 | T-2nd | 8 | 8 | - | - | - | Mike Twardoski |
| 2020 | 11 | 4 | 0 | - | - | - | - | - | 24th | Mike Twardoski |
| 2021 | 7 | 5 | 0 | - | - | - | - | - | - | Mike Twardoski |
| 2022 | 25 | 13 | 0 | T-1st | 12 | 4 | - | - | - | Mike Twardoski |
| 2023 | 28 | 11 | 0 | 1st | 13 | 2 | - | - | - | Mike Twardoski |
NOTE: Final national rankings by American Baseball Coaches Association
*2020 season shortened due to COVID-19*
*2021 season abbreviated due to COVID-19*