Henderson is located in western Chatham County at Georgia State Route 204 (the Abercorn Expressway) to the south, and Interstate 95 to the northwest. Downtown Savannah is 15 miles (24 km) to the northeast.. It occupies a triangular area bounded by Little Neck Road to the northeast,
Henderson Golf Course occupies the southern part of the CDP, with housing developments set around and between the links. Commercial development occupies the southwest corner of the CDP, adjacent to I-95's Exit 94.
According to the United States Census Bureau, the Henderson CDP has a total area of 1.8 square miles (4.7 km2), of which 1.7 square miles (4.5 km2) is land and 0.12 square miles (0.3 km2), or 5.29%, is water.