Gilmer County was formed December 3,1832, from Cherokee County. Several divisions occurred over the years, leading to current boundaries.

The County was named for George Rockingham Gilmer, a Congressional representative from Georgia. Ellijay was selected as the county seat in 1834; it is located on the west bank of the Ellijay River, where this river joins the Cartecay River to form the Coosawattee River.

Early settlements included Mountaintown, Boardtown, Cartecay, Cherry Log, and Talking Rock.

Nearly half the territory of Gilmer County is within the Chattahoochee National Forest and is protected from development by the Federal Government.

Now nicknamed "Georgia's Apple Capital", Ellijay hosts the annual Georgia Apple Festival held in October.