He then at Fort Scott Community College from 1966 to 1969 and then was an assistant coach the University of Missouri from 1969 to 1977.

[5] Charlie Cowdrey became perhaps the only football coach in NCAA history to be fired less than 24 hours after his team had scored a major upset.

The first round the team defeated conference rival Bethel 17–14, and then lost to Northwestern College by a score of 45-23.

[9] About being fired from the post, his son Bruce Cowdrey (also a football coach) related this story: After Southwestern, Cowdrey became the head coach at Morningside College in Sioux City, Iowa[11] from 1993 through the 1995 season.

His teams at Morningside produce 5 wins, 26 losses, and 2 ties during his three years as head coach.