Bowden finished his career first in all-time wins by a Division I-FBS coach with 389 wins. A March 6, 2009 NCAA ruling requiring Florida State to "vacate wins for any games in which an ineligible player participated," threatening to remove as many as 14 of Bowden's wins from the 2006 and 2007 seasons in relation to an academic scandal; Florida State appealed the ruling. The NCAA upheld the ruling on January 5, 2010. Upon final investigation by Florida State University it was determined that Bowden was to vacate 12 wins, bringing his final career record to 377–129–4. At the time, this placed him second to Joe Paterno, coach of the Penn State Nittany Lions. However, sanctions handed down by the NCAA as a result of the Penn State child sex abuse scandal caused all of Paterno's wins from 1998