Zillmere station opened in 1888 at the same time as the line. In 1917, the line was duplicated through the station from Northgate to Petrie. On 23 April 1983, the line through the station was electrified from Northgate to Petrie. In 2000, a third platform opened as part of the addition of the third track from Northgate to Bald Hills.
Zillmere serves the homonymous suburb of Zillmere which was named after Zillman meaning sailmaker and mere meaning marsh or moor.
Zillmere station has three platforms consisting of an island platform and a side platform. Platform 1 is used for inbound services, platform 3 is for outbound services and platform 2 is for some outbound peak services.
Zillmere station has two station entrances which are from either side of the station which are both on Zillmere Road.
Zillmere station does have disability access.
There are bus stops nearby on Zillmere Road and Handford Road serving nearby suburbs. The routes that serve Zillmere are routes 326, 327, 330, N339, P331 and P332.