Police halted all traffic on the commuter line between Stockholms södra and Älvsjö in southern Stockholm at 5.05am after "unauthorized people were spotted in the railway area".
The move caused delays and some cancellations for most commuter trains to and from Stockholm City, including some long-distance trains.
The bomb squad was called in to search the railway area for suspicious objects, but in an update posted online at 9am they confirmed nothing had been found and traffic could resume with knock-on delays.
Police later said they were investigating the incident as possible preparation to commit sabotage, but would not reveal more details. There are no suspects.