The main platform and station building is located to the east of the standard gauge "West" line.

[3] The platform on the standard gauge "east" line runs through a cutting at the Melbourne end of the station.

Alumatta Loop, on the original standard gauge line, used to be to the south of the station, past the Sisely Avenue level crossing, but it was booked out of use in February 2011, and was removed shortly afterwards.

[6] When the Albury - Melbourne standard gauge line was constructed to the east of the station in the early 1960s, extensive works were required to thread it through the former narrow railway reserve.

[11] The works included replacing the original deck with a steel one, covered with a concrete surface, refurbishing the platform shelters, and installing new lighting, fencing, seating and bins.

Wangaratta has two side platforms, but only one is in use due to the Inland Rail project, with upgrade works to start in late 2021.