"We were all running, screaming, and waving at the second train but it continued down the tracks to a full stop like normal," witness Gregory Bane told The Local.
The incident occurred at 6.20pm when an apparently drunk man tumbled onto the tracks in front of horrified bystanders.
Local police confirmed that the 29-year-old man did not survive the collisions.
"I can confirm that he is dead, and that he died on the scene," Anders Lantz of the Flemingsberg police told The Local.
Stockholm public transit operator SL confirmed that the man was hit by two separate trains.
"From what I understand from the accident, the person was first hit by a train from (national rail operator) SJ and in some way bounced to another track where the commuter train hit him," SL spokesman Henrik Palmér told The Local.
Witnesses reported a great deal of confusion and mayhem as the second train approached.
"There was the sound of the heavy freight train on the outer track headed into Stockholm and people started yelling," Bane said.
"He definitely fell. I heard a bang like someone threw something at the side of the train. Men came running toward me as I ran towards the noise. I couldn't see anyone just a grey mass on the tracks when the commuter train going to Stockholm came down the tracks."
The man who ended up on the tracks was "staggering wildly" on the platform, according to Bane, and was seen "yelling and joking" with a friend immediately before the accident.
Police remained tight-lipped about further details.