Warner was hired by the University of Georgia as its new head football coach in 1895 at a salary of $34 per week. For the 1895-1896 academic year, Georgia's entire student body consisted of 126 students. This was Georgia's first year in the Southern Intercollegiate Athletic Association, a conference that it founded along with Alabama, Auburn, Georgia Tech, North Carolina and Vanderbilt. Warner's first Georgia team had 3 wins against 4 losses.
The following year, Georgia rehired Warner and the team had an undefeated season (4 wins and 0 losses). While at Georgia, Warner also caoched Iowa State University. He coached teams from two schools simultaneously on three occasions: Iowa State and Georgia during the 1895 and 1896 seasons, Iowa State and Cornell in 1897 and 1898, and Iowa State and Carlisle in 1899. Warner's Iowa State record was 18-8-0, bringing Warner's total lifetime record to 337-114-32.
After his stint in Georgia, Warner returned to Cornell to coach football for two seasons. He then coached at the Carlisle Indian Industrial School in Pennsylvania from 1899-1903, returned to Cornell for three seasons, and returned again to Carlisle in 1907. During his second tenure at Carlisle, Warner coached one of the most famous American athletes, Jim Thorpe.
In 1914, Warner was hired by the University of Pittsburgh, where he coached his teams to 33 straight major wins and three national championships (1915, 1916 and 1918). He coached Pittsburgh from 1915 to 1923 to a 60-12-4 record.
The next team Warner coached was at Stanford University from 1924 to 1932, where his teams played in three Rose Bowl games, including the classic 1925 Rose Bowl game against Knute Rockne and the Four Horsemen of Notre Dame. Warner added a fourth national championship in 1926.
Warner's final head coaching job was at Temple University where he coached for 5 years until retiring in 1938. He served as advisory football coach for several years at San Jose State College after his retirement from Temple.
Warner brought many innovative playing mechanics to college football:
- the screen pass
- spiral punt
- single- and double-wing formations
- the use of shoulder and thigh pads.