The application was drawn up with national regeneration agency English Partnerships and preferred developer partner Liverpool-based Iliad, on behalf of the Lime Street Gateway Partnership.
The scheme includes a new public space at the front of the station, the demolition of the Concourse Tower and the construction of a new 'landmark' 28-storey mixed-use skyscraper.
The application also seeks to demolish the row of shops at the front of the station to unmask its listed Victorian arched gable-end.
Eliot Lewis-Ward, English Partnerships' area director, said it was promising that the project had reached planning. 'We are delighted, after many months of consultation and design work, to have reached this stage.
'Lime Street is the first impression that many people have of Liverpool and we have a fantastic opportunity to create a new landmark for the city. We hope that the plans meet with public approval,' Lewis-Ward added.