Though Southern was forced to discontinue its baseball program during the uncertain times of the Great Depression and World War II years (specifically from 1932 to 1947), its program was largely stable in the subsequent post-war decades; only four head coaches coached Southern between 1949 and 2017.

In 1987 Southern became the first HBCU to win a game in an NCAA Division I regional tournament by defeating #2-ranked Cal State Fullerton.

In 1996 Southern became the first HBCU to win a game in an NCAA Division I play-in series by defeating Austin Peay.

[28] Due to poor record-keeping by athletic department personnel between 2010 and 2015, 218 student athletes from 15 sports teams at Southern were linked to rules infractions by the NCAA;[29] it is not immediately clear how many, if any, of Cador's 137 wins[citation needed] from that time period may have been vacated by the NCAA.

However, with various unresolved Academic Progress Rate issues, the NCAA limited recruiting efforts, scholarship awards, practice time, and postseason participation for the incoming head coach.

[citation needed] His second team went 32–24[32] (.571), won the SWAC Western Division, the SWAC,[4] the blackcollegenines.com Large School Division HBCU national championship,[3] and qualified for the BCSG 360 HBCU World Series (which was later canceled due to inclement weather).

Notes: *—Flentroy served as acting head coach between the 1976 and 1977 seasons, and Boyd served as acting head coach during the 1977 season; **—up to 137 wins between 2010 and 2015 are subject to be vacated by the NCAA (it is not yet clear how many, if any, of these wins included ineligible players) Notes: *—total includes game forfeited by Prairie View A&M, due to the use of an ineligible player;[39] **—up to 137 wins between 2010 and 2015 are subject to be vacated by the NCAA (it is not yet clear how many, if any, of these wins included ineligible players); §—team ineligible for postseason play, due to a violation of NCAA rules concerning Academic Progress Rate scores;[30] †—game canceled, due to inclement weather;[33] ‡—season canceled by NCAA due to COVID-19 pandemic[35] In 1985 Brock was inducted into the National Baseball Hall of Fame and Museum.

In 2011 Goodwin became the first former HBCU player inducted into the National College Baseball Hall of Fame, and in 2012 Brock became the second.