Police were called to the scene around 3.45pm this afternoon after reports that a teenage boy had been injured.
Details of how he came by his injuries have not been released but it is understood he was not hit by a train.
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A probe has now been launched by police who are appealing to the public for information.
The station has been closed and Scotrail have released updates for passengers.
Trains between Glasgow and Edinburgh have been affected and ticket acceptance has been arranged with Edinburgh Trams between Edinburgh Park, Haymarket and Edinburgh for alternative options.
Scotrail also say passengers travelling from Glasgow Queen Street to Springburn can travel on High Level services from Glasgow Queen Street to Edinburgh via Springburn and Falkirk Grahamston.
A replacement bus service is now running between for Queen Street and Bellgrove.
A Police Scotland spokesperson said: “We received a report around 3.45pm on Saturday, 16 October, that a teenage boy had been seriously injured inside the station on High Street, Glasgow.
“He has been taken to hospital and enquiries are under way.
“The station and the road outside are currently closed to allow emergency services access.
“Anyone who was in the area at the time or has information which may be relevant is urged to contact Police Scotland on 101, quoting incident 2280 of Saturday, 16 October, as soon as possible.”