The Aggies competed at the NCAA Division II level through 2005. At that level, they appeared in the NCAA Division II Baseball Championship 7 times, including two appearances in the College World Series, where they earned fifth-place finishes each time. At the Division I level, the Aggies have made one appearance in the NCAA Division I Baseball Championship, in 2008, where they finished 1–2 in regional competition.[2]
In 2008, future major leaguer Ty Kelly led the Big West Conference with a .397 batting average as a sophomore, and was #2 in the Big West Conference in hits with 94; his career batting average and hits total rank second and third, respectively, in Aggies history.[3]
In July 2021, the entire UC Davis Aggies baseball program was suspended and the coaching staff was placed on administrative leave due to allegations of misconduct.[4] An internal investigation found that players engaged in hazing rituals that included binge drinking, eating live goldfish, strippers, and threats of sexual assault. The team was allowed to resume some activities in October under the supervision of an interim coaching staff.[5] Manager Matt Vaughn resigned in November after the administration found he had failed to address concerns regarding a complaint about hazing from 2018.[6]