The La Crosse chapter of the Rotary International got its start in 1919. The principle individuals involved in starting the local chapter were Otto Schlabach, Edward M. Wing, Percy D. Bentley, Arthur L. Meyers, William A. Jones, Peter J. Yerly and Walter Woods. These men, along with others, met with the president of Madison Rotary Club, Reuben Neckerman, who was sent by Rotary District 15 Governor Burton E. Nelson as his representative to the La Crosse group. During this meeting the first directors of the La Crosse chapter were elected. They were Al L. Guetzman, Edward E. Evans, Otto M. Schlabach, Frank Pittman, Edward M. Wing, Argyle Scott and Bart E. McCormick. The first officers elected were Bart McCormick, president, Edward Wing, vice president, Peter Yerly, secretary, and Frank Pittman, treasurer.

On May 27, 1919, thirty-two charter members were enrolled in the La Crosse Rotary Club, and the charter of the Club was officially accepted on June 1, 1919. The La Crosse Rotary Club, now called "Downtown" Rotary, has either sponsored or been instrumental in starting numerous Rotary clubs: Melrose (1928), West Salem (1948), Onalaska (1960), La Crosse East (1971), Valley View (1980), La Crescent, MN (1982), Prairie du Chien (1986), Viroqua (1987), La Crosse North (1988), Caledonia, MN (1990), and Dubna, Russia (1993).

In August 1987, the first three women were admitted to the downtown Rotary Club. They were Beverly Simone, Anita Froegel, and Pat Heim.

Since 1974, Rotary District 625 (of which the La Crosse club is a part) has sponsored a youth exchange program in which students from District 625 go to live in a foreign country, while students from foreign countries come to live with a family located in District 625. The goal of the program is to promote international understanding and goodwill.

The La Crosse Rotary Foundation was begun in 1983. Contributions are used to help fund area community projects, expanding the scope of service projects with special fund-raising events.

Kids Coulee, a project spearheaded by the Rotary Club, was proposed in 1993. Intended to be a 20,000 square-foot playground with a variety of equipment including slides, swings, bridges, and a sandbox, the playground was to be accessible to all children, even those with disabilities. The Rotary Club sought out not only monetary contributions but also community volunteers who would help build the playground. On September 21, 1994, community volunteers began work on the playground that was dedicated on September 25, 1994.

Seven area Rotary Clubs were involved in the first annual Rotary Lights display in Riverside Park in 1995. Those seven clubs were La Crosse Downtown, Valley View, La Crosse East, La Crosse North, La Crescent, Onalaska, and West Salem. In its first year, 250,000 Christmas lights were used to decorate the park, and approximately 300,000 people walked or drove through to see the display. The display has expanded and changed each year. Every year during the event, the Rotary Clubs collect food donations, which are distributed to local food pantries, and monetary donations that go to local charities.

The group celebrated its 100th anniversary in 2019, and continues to publish a weekly newsletter, Coulee Report.