Middle Branch Chillisquaque Creek is a tributary of Chillisquaque Creek in Columbia County and Montour County, in Pennsylvania, in the United States. It is approximately 5.2 miles (8.4 km) long and flows through Madison Township in Columbia County and Anthony and Derry Townships in Montour County. The creek's watershed has an area of 9.64 square miles (25.0 km2). There are 14.35 miles (23.09 km) of streams in the watershed. Lake Chillisquaque is also in the creek.