The first part of the project involves strengthening three bridges on the approach to the platforms as well as changing the layout of the track and platforms.
John Halsall, route infrastructure director for Network Rail, said: “The project to improve the railway and strengthen the bridges on the approach to Waterloo is an absolutely vital part of our plans to improve capacity at Britain’s busiest station.
“The submission of the planning application to carry out this work is an important step forward and, if approved, we expect to start work before the end of the year.”
The planning application for the proposed work has been submitted to the London Borough of Lambeth.
If permission is granted preparation work would be expected to start in October 2015, with construction taking place between November 2015 and the end of 2016. Associated track and signalling work will then continue until mid-2017.
Tim Shoveller, managing director of South West Trains, added: “We operate one of the busiest railways in Europe, with over half a million passenger journeys every day.
“The biggest investment for decades on our network is well underway but the work to expand London Waterloo is absolutely vital to make sure we can provide much needed extra space, both for our customers now and in the future.”