The train came off the rails between Alvsjö and Stuvsta at around 5am, and passengers were evacuated to another nearby train according to public broadcaster Sveriges Radio.
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Stockholm public transport company SL's press officer told news agency TT that there are no reports of injuries, but there will be disruption to commuter train traffic over Thursday morning.
“How it will impact it is unclear but it will cause trouble,” Fredrik Cavalli Björkman said.
As of 7am trains in both directions were delayed by up to 50 minutes according to SL's live updates on their website. The derailed train will not be moved until Thursday night.