Three sets of boom gates in Cheltenham and Mentone will be gone for good by late 2020.
Early works to remove the level crossing at Balcombe Road are underway, with major construction to begin mid 2019.
The heritage station buildings will be refurbished while work on the new Mentone Station is undertaken. The new station will be 150 metres south, meaning the platforms will be closer to ground level and the rail trench shorter.
Mentone Station gardens will also be upgraded, with the five heritage-listed trees protected in their current spots during construction.
The level crossings at Charman and Park Roads will be removed by lowering the rail line into a trench, with the roads to be rebuilt at their current level.
The new station will have a plaza connecting Cheltenham Park with the shopping area. The existing palm trees will be returned to the station precinct when construction is complete.
The third rail line into Cheltenham Station, which is currently a dead end, will be connected to allow for more trains to run on the Frankston Line once the Metro Tunnel is open.