Shortly before 2am on Saturday, Jefferson County Communications received a call saying a pedestrian had been struck by the westbound train.
According to media reports Mandy Horvath, 21, of Manhattan, Kansas, was found lying on the tracks beneath the train.
A medical helicopter flew to the scene and the woman was stabilised.
According to a report by 10/11 News the woman was in critical condition in hospital.
The Beatrice Daily Star reported that alcohol was believed to be a contributing factor in the incident.