The area of Angera was inhabited in prehistoric times, and artefacts from hunters-gatherers have been found in the cave of Tana del Lupo, on the road that leads to Rocca Borromeo. During Roman times it was an important lakeside port on a trading route for wood and stone via the Ticino river. The current layout of the town centre reflects the Roman town division into districts.
With the arrival of Visigoths in the year 411, Angera was destroyed along with Milan. In the 11th century, it was under the domain of the archbishop of Milan, who built the first fortress on the rock. The building was expanded by the Visconti in the 13th century, and finally became the property of the Borromeo family in 1449, who also bought the town for 12,800 lire. Angera was under Spanish rule for two centuries, and under Austrian government until 1861.