Two young men are said to have torn down an Israel flag at the Basel synagogue and then burned it.
The alleged perpetrators were arrested by the Basel police.
The Jewish Community of Basel (IGB) confirmed the incident to the Swiss news agency Keystone-SDA.
There are camera recordings that show one of the two alleged perpetrators climbing over the fence and taking the flag with him. This was later found set on fire.
The IGB has filed a criminal complaint.