However, the name of the city most likely originated from the Germanization of a Roman place name (Sanctio) (similar to Aachen, Baden-Baden and others), possibly from the name of the Diocletian province Maxima Sequanorum, founded in 297 AD.

In the documents of the 13th century, the Celto-Roman place name was used again as a sign of erudition: 1275 Sigillum Civium Seconiensium = seal of the citizens of the city of Seconis (Seconiis = "at the Temple of Seconia").

The history of the city dates back to the early 6th Century, when Saint Fridolin founded Säckingen Abbey and a church.

Afterwards, construction began in the middle of the town on a Gothic cathedral, called the Fridolinsmünster, which can still be visited today.

In the closing stages of the 1672–1678 Franco-Dutch War, the town was severely damaged by French soldiers commanded by the Comte de Choiseul, following their victory over an Imperial force at Rheinfelden on 7 July 1678.