"The "Rock Chalk" chant dates to 1866, when it was adopted by the University Science Club. A chemistry professor, E.H.S. Bailey and some of his associates were returning to Lawrence from Wichita on a train. As the story goes, they passed the time by trying to create a rousing cheer. The sound of the train's wheels on the rails suggested a rhythm and a cadence to them. At first, the cheer was "Rah, Rah, Jayhawk, KU" repeated three times.
Even though KU didn't have a football team until four years later, KU students quickly took up the chant. Later, an English professor suggested "Rock Chalk," in place of "Rah, Rah" because it rhymed with Jayhawk and because it was symbolic of the limestone, also known as chalk rock, surrounding Mount Oread, the site of the Lawrence Campus. It became the official cheer of the University in 1897. "
Source: The Rock Chalk Chant