This town stands on the upper Lombardy plain, on the southern outskirts of Brianza. The municipal area is almost totally urbanised, with the exception of farmland in the east and south, part of the Grugnotorto Villoresi Park, and some areas along the Seveso river, which runs through the city from north to south. Another waterway running through Paderno Dugnano is the Villoresi canal, which is close to the border separating Paderno Dugnano from the municipality of Varedo.

Paderno Dugnano is a town on the outskirts of Milan and lies approximately 10 kilometres north of Piazza del Duomo as the crow flies.