Shortly after 1:30pm Bern police were informed of a bomb alert at the nearby Holy Spirit church, a police statement said.
Officers were sent to the scene and noticed a man behaving strangely.
"Initial information has identified him as an Afghan man," police spokesman Ramona Mock told AFP.
The young man was arrested and all those inside the church were allowed to leave, but the area remained closed for several hours, police said.
Two suspicious objects found in the man's possession were rendered harmless, the police statement added. There was no explosion or any injuries or damage.
Rail traffic was not affected but passengers were required to use an alternative entrance to the station.