Claremont began competing in the SCIAC in 1947-48 when Pomona College and Claremont Men’s College combined to form one athletic team (Pomona had been competing by themselves since the SCIAC’s inception in 1915). Pomona - Claremont competed in the SCIAC for 11 years and during that time the team won 25 SCIAC titles. In 1958-59 Claremont Men’s College combined with Harvey Mudd College and began competition as Claremont-Mudd. The team was ineligible for SCIAC championships until 1959-60. The team continued as this entity until the SCIAC began sponsoring women’s sports in 1976-77 at which time it became Claremont-Mudd-Scripps (Claremont Men's College became Claremont McKenna College in 1981). The men’s program has won 160 SCIAC titles since its inception. This is more than any other SCIAC school during this same period by 38. The women’s program has won 71 SCIAC titles which is the second most among SCIAC schools. Claremont-Mudd-Scripps is the only team in the SCIAC which has won a conference title in each sport and they have won all 19 sports at least twice. Each of the men's teams has repeated as SCIAC champion at least once and have each won at least four titles. Seven of the women's teams have repeated as SCIAC champion.

The SCIAC All-Sports Competition began in 1972-73. This competition awards points to schools based on their finish in the SCIAC standings. In the 37 years of the competition Claremont-Mudd(-Scripps)’ men’s program has won the award 32 times. With the addition of the women’s programs in 1976-77 the competition was expanded to include the women’s sports as well as an overall competition. The women have won 15 All-Sports Trophies including 13 of the last 17. The combined Claremont-Mudd-Scripps athletic program has won the All-Sports Trophy 21 times with victories in 20 of the last 24 years. 2008-09 was another successful year as seven sports won SCIAC titles and six sports finished second or third.

Only one other school has won as many as six SCIAC men’s titles in one academic year while CMS has won six or more five times. The most men’s titles CMS has won in one year is eight in 1989-90. CMS is the only school to win six SCIAC women’s titles in one year which the Athenas achieved in 1998-99. The combined program has won as many as 10 SCIAC titles in one year (1987-88 & 1998-99) and has won nine titles four times. No other program has won more than eight in one year.

In addition to their strong showings in the SCIAC the Claremont-Mudd-Scripps athletic program has also performed well in post-season competition. CMS has won two national titles. Claremont-Mudd won the NAIA swimming crown in 1967 and the Claremont-Mudd-Scripps men’s tennis team tied for the NCAA title in 1981. The men’s swimming and tennis teams have also combined to win 11 second place trophies at the NCAA championships. In addition, men’s soccer was the NCAA runner-up in 1983. Overall 19 of the 21 CMS sports have competed in the post-season and 17 have finished in the top 17 including 13 in the top 10.

In 1995-96 the National Association of Collegiate Directors of Athletics began their Director’s Cup Competition for Division III institutions. This competition is similar to the SCIAC All-Sports competition except that points are earned based on national results rather than conference and that there are over 400 eligible schools instead of eight. Claremont-Mudd-Scripps has finished in the top 60 12 times with nine finishes in the top 40, six in the top 30, four in the top 20 and a best of eighth. These have been among the best showings by small colleges and was the best result by a SCIAC school nine of the 14 years.