The fire broke out late on Sunday and 120 firefighters were still fighting the flames on Monday morning, but the blaze was mostly under control.
The cause of the fire, which started at a store inside the Onkel Toms Huette station in the city's south-west Zehlendorf neighbourhood, was not immediately known.
The fire quickly spread to two other stores and several people living nearby had to leave their homes because of the smoke, German news agency dpa reported.
Berlin Fire Department said the person who was seriously hurt was flown by helicopter to a clinic. Three others, including a child, suffered from mild smoke inhalation and were treated on-site, dw.com reported.
The fire department earlier tweeted that a shop and the roof of the train station were burning.
