Flinders Street Station will get a $100 million facelift, including a restoration of its fabled but decaying ballroom.

The station's leaking roof will be repaired and passenger facilities, including toilets, will be modernised in a project the state government estimates will take four or five years.

Premier Daniel Andrews announced the $100 million project on radio station 3AW on Wednesday morning.

"It needs to be restored to its former glory … The way it looks now, I don't think anybody can be proud of it," Mr Andrews said.