Pagsanjan has a land area of 26.4 square kilometres. It is located about 92 kilometres (57 mi) southeast of Manila. It is bounded on the east by the Balubad Mountain; on the west by the capital town of Santa Cruz; on the north by the San Isidro Hill and Laguna de Bay; on the north-east by the town of Lumban; on the southeast by the towns of Cavinti and Luisiana; on the south by Mount Banahaw; and on the south-west by the town of Magdalena.