Captain Matthew Ketchum, Colonel William Bullock, and Nicholas Clark are credited with settling the area in 1769; Clark later became Clarksburg's namesake. The town began as a mostly agrarian community, with mills springing up along the waterways in the nineteenth century. The major mills were one to make cashmere, and several mills supplied gunpowder during the Civil War. However, the industry was stopped by the town after one of the mills exploded in 1869.

According to the United States Census Bureau, the town has a total area of 12.8 square miles (33 km²), of which 12.8 square miles (33 km²) is land and 0.1 square miles (0.26 km²) (0.62%) is water.

Clarksburg is located at 42°42'42.86"N,73°05'02.97"W. Clarksburg is bordered by Pownal and Stamford, Vermont on the north, Florida on the east, North Adams on the south, and Williamstown on the west.

The town is bordered on two sides by mountains, with East Mountain and Bald Mountain to the west, and the Hoosac Range to the east. Between the two ranges, Hudson Brook and the north branch of the Hoosic River flow through the valley, merging just south of the town line. In the northern part of the valley is Clarksburg State Park, operated by the state's Department of Conservation and Recreation. The park is home to Mauserts Pond and offers picnicking, hiking, and camping, as well as other recreational activities. On the Vermont side of the border lies the Green Mountain National Forest. The Appalachian Trail crosses from north to south through the town, passing just west of the peak of East Mountain, the highest point in town, at 2,300 feet (700 m).

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