In 1887, a junction was provided for construction trains on the new Kilmore line, which branched off to the west of the station, passing behind the Down platform, with the points facing Melbourne. In 1888, a signal box named Kilmore Junction opened on the eastern side of the main line, but a station was not provided until March 1890. It had only small passenger shelters and no goods facilities. Even though the branch line was extended north-west to Heathcote, and thence to Bendigo in 1890, the station was not renamed Heathcote Junction until 15 May 1922.