According to the United States Census Bureau, the township has a total area of 13.6 square miles (35.2 km2), all land.

Pequea Creek, a southwestward-flowing tributary of the Susquehanna River, forms the southern border of the township.

Unincorporated communities in Pequea Township include New Danville, West Willow, Baumgardner, Burnt Mills, Herrville, and part of Willow Street.

At the time of the 2000 census, there were 4,358 people, 1,581 households, and 1,263 families living in the township.

16.2% of households were made up of individuals, and 6.3% were one person aged sixty-five or older.