According to the United States Census Bureau, the township has a total area of 48.8 square miles (126.3 km²), of which, 48.4 square miles (125.4 km²) of it is land and 0.4 square miles (0.9 km²) of it (0.74%) is water.
Middlebury Township is bordered by Farmington Township to the north, Tioga and Richmond Townships to the east, Charleston and Delmar Township to the south and Chatham Township to the west.