The owner had lent the precious instrument to a musician friend who took it on a train on Friday but forgot it when he got off at Bern, police said.
After a fruitless search by train staff, surveillance cameras spotted a passenger walking off with the violin at a different station and police launched an appeal for help.
The violin turned up on Sunday in the lost-property office at Bern station.
Police did not disclose the names of anyone involved, nor the value of the instrument.
Around 600 violins made by Italian master craftsman Antonio Stradivari are still in existence. One fetched about €11 million ($13.5 million) in a 2011 charity auction for victims of the Japanese tsunami.
In 2008, a US violinist left a $4-million (€3.2-million) Stradivarius in the back of a New York cab. The cabbie returned the violin to its owner.