Since 2000, the winningest programs in college football The Nittany Lions of Penn State are ranked 20th in the country (144-82). The winning percentage is 0.637. Auburn Tigers (154-74; 0.675 winning percentage)Auburn Cardinals (154-74; 0.675 winning percentage) Miami Hurricanes 17, (154-73;.6784 winning percentage) LSU and Clemson will face off for a chance to capture the 2019-20 national title. Since the 1936 season, the following colleges have won the most national championships in college football. Alabama earned their first national championship in the poll era in 1961, followed by back-to-back championships in 1964 and 1965.