The main entrance to Melbourne's historic Flinders Street Station will be redesigned as part of a $100 million project to restore the crumbling building.

Repairs and renovations are due to start within weeks, including fixing the leaky roof, restoring the station's facade, repainting the 106-year-old building, retiling dirty walls and refurbishing the dingy toilets.

The interior of the Swanston Street entrance will be remodelled to ease the commuter crush at peak-hour, in preparation for the creation of the adjoining CBD South station as part of the $11 billion Melbourne Metro Rail Project.

Premier Daniel Andrews said Flinders Street Station was in desperate need of an upgrade. ( ABC: Robert Baird )

New station entrances will be built at the western end of the station near Elizabeth Street and in the Degraves Street subway.

Premier Daniel Andrews said the work would bring a "modern touch" to the building, which was falling apart.

"This is a real gem, it's a great part of our story, the heritage of our city, but it's showing its age and it desperately needed this upgrade," he said.

Flinders Street Station's famed ballroom is not part of the restoration project, but the State Government is considering proposals for it to be opened for housing, crisis accommodation, restaurants and retail.

Around 200,000 commuters pass through the station every day, making it Melbourne's busiest.

The project is due to be completed in 2018.