Officials said the crash occurred east of downtown, near Sampson Street and McKinney, just before midnight.
HPD told ABC13 that it is unclear why the woman, who is in her 40s, was parked on the railroad tracks with her two dogs inside the vehicle.
RELATED: Traffic delays expected after train clips car, inspection underway, Sugar Land PD says
The train that collided with her car was a Union Pacific freight train.
The woman was taken to the hospital and is expected to be OK. Officials said the woman's dogs were taken to a nearby shelter.
HPD said no other injuries were reported, and the railroad has since been reopened.