Arlanda Express informed passengers on Thursday morning that all its services both northbound and southbound were cancelled.
Service was resumed later in the day, with trains leaving at 15 minute intervals but with some slight delays.
Train services between the Stockholm suburbs of Ulriksdal and Helenelund suffered long delays after the high-speed train to Stockholm's main Arlanda Airport left the tracks just north of Ulriksdal at around 7am on Thursday morning.
The train was travelling at a low speed as the driver had been instructed to check a gauge but the heavy snowfalls caused one of the train's wheelsets to slip onto the wrong side of the track leaving the train stationary.
None of the passengers were hurt in the incident and are set to be evacuated to another Arlanda Express train.
The derailment meant that two of the four tracks leading past Ulriksdal north of the city were closed and resulted in delays on the Märsta-Södertälje and Västerhaninge-Bålsta commuter services as well as Uppsala services.
The heavy overnight snowfalls caused widespread problems across the Stockholm transport system on Thursday.
Stockholm Public Transport (SL) reports that in addition to the delays to commuter train services, there are extensive delays to bus services, especially in Nacka/Värmdö and Södertälje, but warns that problems may occur on all routes.