Settlement of the Malvern area began in 1837 when John Gardiner took up a grazing run near the creek that later came to bear his name.
Crown land was first sold in 1840 and in 1854 land was made available for purchase in the Gardiner township. The Gardiner District Road Board was formed in 1856 and became the Gardiner Shire Council in 1871.
Gardiner became Malvern in 1878 and the following year a rail service to Malvern Station began. The current railway station was completed in 1914.
The foundation stone of the Shire Hall was laid in 1885 and the official opening of the completed building took place in 1886. Additions and extensions of the Town Hall were later undertaken.
In 1890 the Stonnington mansion was constructed by John Wagner, a proprietor of Cobb and Co coaches. From 1901 to 1931 the building was used as the residence of seven Governors of Victoria.
Malvern was proclaimed a City in 1911. In 1994 the City of Malvern became part of the City of Stonnington, which is comprised of the suburbs of Armadale, Glen Iris, Kooyong, Malvern, Malvern East, Prahran, South Yarra, Toorak and Windsor.