Tenants of the building were evacuated. One of the train cars was suspended in midair. The woman, who works as a cleaner and was the only person injured, was flown by helicopter to Karolinska University Hospital.
An investigation was underway. Tomas Hedenius of train operator Arriva told broadcaster TV4 that it appeared that the cleaner, who was in her 20s, had stolen the train while it was in a depot. There were no passengers onboard.
The crash occurred at Saltsjobaden, the end station on the local Slussen-Saltsjobaden line. The accident took place around 02:30 (0130 GMT) when no trains operate the line.
Christer G Wennerholm, public transport commissioner at the Stockholm County council, ordered a review of "security routines".