Once the American Civil War began in 1861, Buffalo Academy was used by both Union and Confederate armies as headquarters, hospitals, and barracks. After war broke out, many of the students enlisted. The location was contested repeatedly as a strategic location in the Kanawha River valley, much the same as nearby Eleanor and Red House.
After the Civil War, the building itself required extensive repairs before education could resume. By the 1920s it was a part of the Putnam County school system, where it served as the high school until 1952. It is currently empty, although the local historical society has taken responsibility for the grounds and members hope to preserve the building which is part of the Buffalo Town Square.