British Transport Police confirmed she died during the night, having been in intensive care in Sheffield since the crash.
It happened just before 2pm on Beech Hill Crossing, Springs Road, Finningley, near Doncaster, on Tuesday 4th December.
The girl has has been named at Emma Lifsey from Haxey in North Lincolnshire.
The car driver, a 67-year-old woman was taken to hospital with minor injuries.
Around 20 passengers were evacuated from the train, which was the 11.54am East Midlands Trains service from Lincoln to Doncaster.
No-one on the train was injured.
“Our first priority and thoughts are for those involved in the incident,” said David Horne, managing director of East Midlands Trains.
“Our staff ensured that passengers were safely escorted from the train.”
“We will work with Network Rail and the British Transport Police to ensure those involved in this incident are given every assistance.”
“Safety is our absolutely priority and we will do everything in our power to assist the investigation into identifying the cause of the incident.”
Train services continue to be replaced by buses between Lincoln and Doncaster on Wednesday 5th December.
For up to date travel information go to: www.eastmidlandstrains.co.uk