The application follows a public exhibition staged by Network Rail in October, during which the plans were seen by more than 2,000 people.
The project will transform Birmingham New Street station into a modern transport hub that is expected to provide more than £2bn in economic benefits for the city.
The project’s first phase involves building a new concourse, to be opened in 2012, over what is now a lower-level car park.
During the second phase the concourse’s size will be increased by three-and-a-half times, doubling passenger capacity.
The project is expected to finish in 2015.