Rusnė was first mentioned in historical sources in the 14th century. In 1419 the first church was built in Rusnė, and in 1553 a Lithuanian parish school was established. In 1863 the Rusnė synagogue opened.
In 1946 Rusnė received municipal rights, and in 1967 the whole Island of Rusnė was given this status.
Rusnė town and Rusnė island is very popular place for angling, as Nemunas delta is rich in various kinds of fish, and tourism infrastructure is built up in recent years. It is also a popular place for birdwatching.