F�ssen was settled in Roman times, on the Via Claudia Augusta, a road that leads southwards to northern Italy and northwards to the former regional capital of the Roman province Raetia, the capital of which was Augusta Vindelicum (today's Augsburg). The original name of F�ssen was "Foetes", or "Foetibus" (inflected), which derives from Latin "Fauces", meaning "gorge", probably referring to the Lech gorge. In Late Antiquity F�ssen was the home of a part of the Legio III Italica, which was stationed there to guard the important trade route over the Alps.
F�ssen later became the site of the "Hohes Schloss" (High Castle), the former summer residence of the prince bishops of Augsburg. Below the Hohes Schloss is the Baroque complex of the former Benedictine monastery of St. Mang, whose history goes back to the 9th century. F�ssen has Saint Mang (Magnus of F�ssen) as its patron saint. His original burial place was in the small chapel he built. His bones were transferred to the crypt of the church built in 850. Around the year 1100 all his bones disappeared.
In 1745, the Treaty of F�ssen was signed between the Electorate of Bavaria and Habsburg Austria, ending Bavaria's participation in the War of the Austrian Succession.
During the 19th century, composer Richard Wagner used to come to F�ssen by railway when he visited King Ludwig II of Bavaria.
Under the Nazi Party, F�ssen was within the administrative division of Gau Swabia. During World War II, a sub-camp of the Dachau concentration camp was located in the town.
Since the 1950s the town is familiar to travellers as the southern terminus of the Romantic Road.
The Likatier tribe, an Intentional community, was founded in F�ssen in 1974. F�ssen was host to the 1988 World Junior Curling Championships
