As a sophomore, Eller helped lead the Gophers to a Rose Bowl victory. While Eller shared the starting position as a sophomore he became a full-time, two-way player as a junior and senior and was voted All-America both years. During his time in college the Gophers were National Champions as well as Big Ten champions. As a senior (1963) Eller was the runner-up for the Outland Trophy. Following each football season, the Carl Eller Award is given to the University of Minnesota's Defensive Player of the Year. He was elected to the College Football Hall of Fame in 2006.
Starting in 1968, Eller's fifth campaign, Minnesota won 10 Central Division titles in the next 11 seasons. The Vikings won the 1969 NFL championship and NFC crowns in 1973, 1974, and 1976 and Eller was one of 11 Vikings to play in all four of their Super Bowls, all losses.
He was selected to play in six Pro Bowls (1968–1971, 1973, and 1974). After being traded with an eighth round pick to Seattle Seahawks for defensive tackle Steve Niehaus, Eller played his final season in 1979 with the Seattle Seahawks, where he ran his career total to 225 games. In his career, "Moose" only missed three games and started 209 out of the 225 he played.
Eller is credited as the Vikings all-time sack leader with 130½. He also had 3 sacks with Seahawks in 1979 for a career total of 133½. He set career-high 15 sacks in 1969 and then matched that total in 1977, also to his credit 7 seasons with 10 or more sacks.
Eller was First-team All-NFL from 1968–71, and again in 1973. He was also Second-team All-Pro in 1967 and 1972 and was All-NFC by AP and The Sporting News in 1975. Matched with his Pro Bowls, Eller had a nine-year consecutive streak with some sort of post-season honor which began in 1967 with his Second-team All-pro selection and ended in 1975 with his All-NFC honors.
As a licensed drug and alcohol counselor, Eller founded a group of substance-abuse clinics in the Twin Cities called Triumph Life Centers in 1986. He obtained a college degree in Human Services from Metropolitan State University in 1994 and went on to work for the Minnesota Department of Human Services, addressing issues of health disparities between white people and people of color.
Eller has previously acknowledged personal problems with substance abuse, and he has spoken openly and publicly to groups about the problems of chemical dependency.
Eller was arrested in 2006 for DUI and pled guilty.
Eller was arrested again in 2008 for fourth-degree assault of a police officer and second-degree refusal to submit to chemical testing, both gross misdemeanors. Eller was sentenced and served 60 days in the county workhouse.
Eller has now teamed up with David Gergen, President of Pro Player Health Alliance, to help promote sleep apnea awareness. Together they have done radio and TV appearances and events across the country. They are planning a Super Bowl Symposium to spread the awareness of sleep apnea and concussions in Scottsdale, AZ January 27. With them will be Dr. Reyes, the head neurologist for the United States military.