A woman, believed to be in her 30s, was caught under the train at Eagle Junction railway station just after 12pm Wednesday.
Emergency services reportedly freed the woman at 12.55pm.
A Queensland Ambulance Service spokeswoman said the woman is currently conscious and has lower leg injuries, as four fire crews continue their rescue efforts.
QAS said the woman was taken to the Royal Brisbane Hospital in a serious condition.
The incident is said to affect the flow on rail commuters travelling through the region, with Airport and Doomben trains experiencing delays of up to 40 minutes.
Police said they are treating the incident as one of self-harm.