Wacona was built in 1922 to replace the Pine View-Jamestown Consolidated School and included an elementary and a high school. The name "WACONA" is unusual. The story is told that when the class of 1922-23 began the first yearbook, the idea of titling it "Pine View-Jamestown Consolidated" just didn't click. Miss Eddie Mae Barrett, one of the yearbook advisors, suggested "Ware County, North America." That clicked when it was shortened to its acronym, "WACONA." Since that time the school has used that name, but few students, even today, know how the school got its name. Tragedy struck the school on December 5, 1926, when the building mysteriously burned. Some reported that only the brick shell remained but the community saved the day. Area churches became schools until, on January 29, 1927, when the building, adorned in stucco, appeared as the landmark it is today.
An additional change was made in 1958 when the Ware County High School was built and consolidated the last two remaining high schools in the county, Wacona and Waresboro, leaving Wacona as an elementary and junior high school. A new building was completed in 1987 and, even though the old structure remains, Wacona students do not use it except for the auditorium.
Wacona remained an elementary and junior high school for several years. One by one the junior high grades were moved to other schools. The final move was made in 1995 when the sixth grade was transferred to the middle school. In the late 1980s full day kindergartens were placed in all the schools and today Wacona serves approximately 600 students in kindergarten through fifth grade.