On December 15, 1964, the Calhoun-Clemson School on College Avenue and 123 burned during the early hours, destroying all but the lunchroom and new wing. For the next two years, classes were held on the Clemson University campus, at Central Elementary, in portables, and in what was left of the old building. Students were bussed to the cafeteria from all locations for lunch. In spite of scattered locations and other hardships, the school flourished with the leadership of Principal Clif Harkey.

To replace the burned Calhoun-Clemson School, construction began at Highway 123 on Frontage Road. More than 600 students and 20 teachers moved into the new building, called Clemson Elementary, in August of 1966. On January 22, 1967, the school was named Margaret Morrison Elementary School in honor of "Miss Maggie," a life-long resident of Clemson. Miss Morrison taught for 36 years in the area and retired as principal of Calhoun-Clemson School.

After integration in 1970, the students Calhoun Elementary on Butler Street moved to Morrison Elementary; the building on Butler Street, known as the Morrison Annex, was used to house primary grades. At this time there were 1,050 students in grades one through eight. One year later, the seventh and eighth graders moved to the newly opened R. C. Edward Junior High School.

In the 1979-1980 school year, Morrison Elementary was one of three elementary schools in the state to be chosen as "Palmetto's Finest," an award recognizing academic excellence. Since that time our school has been a finalist for the "Palmetto's Finest" three times.

By the 1990's Morrison Elementary School and the Morrison Annex had outgrown their buildings. On November 16, 1999, ground was broken on Berkeley Drive for a new school building. To return to the tradition of community, the name Clemson Elementary was chosen for the new school. Students and teachers moved into the building in August of 2000 under the leadership of Principal Paul Prichard, who was named in 2001 by the governor of South Carolina the first South Carolina Year of the Child Hero.