The man was on the tracks around 8.20pm on Monday at the Kungsträdgården station in the centre of the capital.
"It was an accident and we don't know how it happened," Björn Svensson, officer at the command centre, told the Aftonbladet newspaper.
The man was seriously injured in the incident, but was still able to communicate, police said. Officers have still not managed to find any witnesses.
Traffic between Kungsträdgården and Fridhemsplan was shuttered throughout the evening during the police investigation, but was up and running again after a few hours.
The man, who police said was a young man likely on the tracks to spray graffiti, got an electric shock from the power cables by the tracks before he was hit by the train.
"He was dragged along by the last carriage. He got a serious shock, and is at the hospital, and is quite seriously injured," added Johan Jönsén of the Stockholm police.
In September, another man was hit by a train in Stockholm and the incident made world headlines after security footage showed a thief picking the victim's pockets before the train hit.
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