First settled in the 1760s by soldiers from nearby Fort Pownall, Frankfort is the oldest town on the Penobscot River. At the end of the French and Indian War, the Penobscot Valley had become part of Massachusetts, which led to the first cautious encroachments by English settlers on lands that had belonged to the Penobscot Indians, a process that began with Franfort.
The town was incorporated on June 25, 1789, and named for the German city. Frankfort was once much larger than it is today, as it originally included the current towns of Winterport, Stockton Springs, Monroe, Prospect, part of Hampden, and part of Swanville, the major settlement area being what is now Winterport.
Bombed by the British in 1814, Frankfort was once a shipbuilding community, its main village, as it is today, is located at the confluence of the North and South branches of the Marsh River, which flow into Marsh Bay. Mount Waldo overlooks the Mendall Marsh. The North Branch of the Marsh River flows through the village, which is clustered tightly at the point where US Route 1A crosses the river.