A Whitman College Athletics Association formed in 1886, due in part to a desire of students to participate in baseball. The first football team was formed in 1892. Women's basketball was being played as early as 1897, and tennis was a popular early activity. The arrival in 1906 of Raymond Vincent Borleske was a seminal moment in the development of Whitman athletic programs. Borleske was considered the greatest football running back in the West during his playing days. Borleske graduated in 1910 and returned in 1915 to teach and coach, becoming the dominant figure in Whitman athletics until 1947.

Whitman College was one of the original members of the Pacific Northwest Intercollegiate Athletic Conference (PNIAC), which, at the time of its conception in 1910, contained schools such as the University of Washington, University of Oregon, and Washington State College, later Washington State University. In later years, most of the larger schools withdrew, leaving Whitman, College of Puget Sound, Linfield College, and Pacific University, all of which belong to the present-day Northwest Conference. Willamette University, Pacific Lutheran University, George Fox College, Lewis and Clark College and Whitworth University have since joined the conference, leaving its present membership at nine institutions.

Whitman dropped football in 1977, but still competes in intercollegiate cross country, tennis, volleyball, swimming, golf, basketball, and baseball, as well as maintaining an active intramural program. Nationally, Whitman was originally a member of the National Association of Intercollegiate Athletics (NAIA) and is currently a member of the National Collegiate Athletic Association (NCAA) Division III.