Bomb technicians were called in to search the area and there were severe delays both to commuter trains and national rail services.
Victor, one of the many commuters affected by the delays, told Radio Sweden:
They're saying there's a bomb threat somewhere in Stockholm so all trains are standing still. If I go by bus now, it will take 2.5 hours for me to get to work."
While train traffic has been resumed, the delays are expected to last several more hours.