The town was set apart from the Town of Fayette in 1803. Junius was subsequently divided to form new towns: Wolcott, in Wayne County (1807), Galen also in Wayne County (1812), Seneca Falls (1829), Tyre (1829), and Waterloo (1829).
The Cobblestone Farmhouse at 1027 Stone Church Rd., Cobblestone Farmhouse at 1111 Stone Church Road, Cobblestone Farmhouse at 1229 Birdsey Road, and John Graves Cobblestone Farmhouse are listed on the National Register of Historic Places.
According to the United States Census Bureau, the town has a total area of 26.9 square miles (70 km2), of which, 26.7 square miles (69 km2) of it is land and 0.1 square miles (0.26 km2) of it (0.41%) is water.
The New York State Thruway (Interstate 90) passes across the town. New York State Route 318 is an east-west highway in the town running parallel to the Thruway. New York State Route 414 is a north-south highway crossing a few arces in the far north-eastern part of Junius.