Cooper began his coaching career in 1962 as the freshmen team coach at Iowa State. He then was an assistant coach at Oregon State from 1963 to 1964 under Tommy Prothro and helped Oregon State finish first place in the Athletic Association of Western Universities (AAWU) in 1964. Oregon State also made the Rose Bowl and finished #8 in the final AP Poll. Cooper then followed Prothro to UCLA to be an assistant there from 1965 to 1966. In the 1965 season, UCLA finished first in the AAWU and #4 in the final AP Poll and won the Rose Bowl. The 1966 UCLA team finished #5 in the AP Poll.