He played for the Ole Miss Rebels of the University of Mississippi, and was elected to the College Football Hall of Fame in 1997.

As a high school sophomore, his Marianna High School coach Bill Landers took him to a University of Mississippi (Ole Miss) football game, and introduced Flowers to Ole Miss coach John Vaught.

Flowers took particular pride in the fact that 42 of the team's 43 players graduated, and many earned considerable achievements in their lives.

[4][6] The team was ranked number 2 at the end of the season, behind 10–0 Syracuse,[10][11] which Flowers believed was because of the one loss to LSU.

He blamed himself for missing the tackle on LSU Heisman Trophy winner Billy Cannon[11] that allowed the one, winning, touchdown in the game.

However, in order to retain his eligibility to play in the Sugar Bowl, he requested to keep the contract a secret until January 2, 1960.

Wellington Mara accepted this request and the team did not submit the contract to league commissioner Pete Rozelle for approval.

The team moved to San Diego the following year, and Flowers started 9 games, but still only had 51 rushing attempts (to go along with 16 receptions).

After moving to Atlanta in 1965, he sold municipal bonds for various large firms, eventually holding the position of vice-president, until his retirement.

[7] After his death, the Charlie Flowers Leadership Fund for Athletics was established at Ole Miss, aimed at student-athletes.