From Wikipedia:
The cult chant was first adopted by the university's science club in 1886. Chemistry professor E.H.S. Bailey and his colleagues were returning by train to Lawrence after a conference. During their travel, they discussed a need of a rousing yell. They came up with "Rah, Rah, Jayhawk, Go KU"[1], repeated three times, which later became "Rock Chalk Jayhawk, KU".
By 1889, "Rock Chalk"—a transposition of chalk rock, a type of limestone, that exists in Kansas, but only in the Cretaceous-age bedrocks of central and western parts of the state (more than 150 miles west of Lawrence)