In 1900, Williams was hired as the head football coach at the University of Minnesota, where he invented the Minnesota shift.[2] His Minnesota Golden Gophers were Big Ten Conference champions eight times (1900, 1903, 1904, 1906, 1909, 1910, 1911, 1915). Williams had a 136–33–11 record at Minnesota. His winning percentage (.786) is the highest of any Gopher football coach to date with the exception of Wallie Winter who went 6–0 in his only season 1893. In 1903, the Gophers went 14–0–1. Their lone tie came against Fielding H. Yost's Michigan Wolverines. After the contest, the Wolverines left behind their water jug at Northrop Field, which gave rise to the Little Brown Jug, one of the oldest and most famous college football trophies.
Williams was inducted into the College Football Hall of Fame with the inaugural class in 1951. Williams Arena, the home venue for Minnesota basketball, was renamed in his honor after a remodeling in the 1950s.