San Zeno Naviglio (Brescian: Sàn Zé) is a town and comune in the province of Brescia, Lombardy.

The first documented town was established in the 15th century; the locality was called Tregonzo or Tregoncio which derives from Latin Inter Gurgites.

In the ephemeral Napoleonic Repubblica di Brescia (1797), the commune belonged to the Cantone della Garza Orientale.

During the Napoleonic dominion, the commune was abolited: town was administrated by Brescia directly.

In 1881 during an administrative reform of the Kingdom of Italy, the commune was renamed San Zeno Naviglio.