Stanford won the 2016-17 Division I Learfield Sports Directors' Cup, extending its streak to 23 consecutive seasons of capturing the award presented to the most successful intercollegiate athletic department in the nation.
The Cardinal won the trophy even without the points baseball would have added for qualifying for the postseason.
Men's soccer head coach Jeremy Gunn accepted the award during the annual National Association of Collegiate Directors of America conference in Orlando.
Stanford compiled 1,536 points, with Ohio State (1,391.75), USC (1,251.25), Michigan (1,174.25) and Florida (1,152.50) rounding out to the top five.
Oregon finished eighth and UCLA was ninth in the complete standings.
The Learfield Sports Directors' Cup was developed as a joint effort between NACDA and USA Today. Points are awarded based on each institution's finish in up to 20 sports, 10 women's and 10 men's.
Stanford claimed five national championships during the past academic year, increasing its overall total to 137.
Of Stanford's 137 championships, 113 are NCAA titles, including recent crowns in men's soccer, women's volleyball, women's swimming and diving, and women's water polo. Stanford last won four NCAA titles and five national championships in 2001-02. The Cardinal and UCLA share the NCAA lead with 113 titles.
The Cardinal also captured its seventh IRA lightweight rowing title in the past eight seasons.
The Cardinal has won at least one NCAA title in each of the past 41 seasons, representing the longest streak in the nation.
Division I Learfield Director's Cup
2, Ohio State
6, North Carolina
7, Penn State
14, Texas A&M
17, Florida State
19, South Carolina
21, Notre Dame