A 45-year-old woman was also injured as a result of the blast, Stockholm police told Swedish news agency TT.
Reports about the incident came at 10:07 GMT on Sunday and now the metro station is shut and the scene is cordoned off by the police.
No preliminary information on background of the blast is available, however, according to officials, the explosion is not believed to be a terror act.
People on social media have posted photos and videos from the blast area.
Varby Gard train station is on the part of the metro's T13 line, which connects southern suburbs to the centre of Stockholm.
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