Emergency services descended on Crossmyloof Station, in the South Side of the city, at around 8.15 am, after reports of a fire onboard a train carriage.
Eyewitnesses reported seeing a carriage on fire and the area around the station was evacuated.
Commuter Laura Ferrier tweeted: "Sitting on the train waiting for it to leave to go to Uni and they say it's delayed cos of a fire... Suppose I'll just need to go back to bed."
Hannah Cochrane tweeted: "Train on fire at crossmyloof telling us the delay could be up to 2 hours."
Paul Sutherland tweeted: "A train is on fire at Crossmyloof. All the trains are aff. Some day for it eh?"
Scottish Fire and Rescue confirmed they were in attendance at the scene.
However, a spokeswoman added: "No further information is available at this time."
A Police Scotland spokeswoman said: "We were notified of a report of a train carriage on fire at Crossmyloof station at 8.15am today."
Train operator ScotRail confirmed services between East Kilbride and Glasgow Central were cancelled.
A spokesman said: "We apologise to customers for any inconvenience this incident has caused to their journeys this morning."
Meanwhile, services between Milngavie and Motherwell were delayed for an hour this morning due to flooding between Milngavie and Westerton. Milngavie to Edinburgh services were also delayed.
Scotrail has confirmed that normal service is now resuming, tweeting: "Train services between Milngavie and Motherwell are also returning to normal, but may still be delayed."