In 1921 Captain D S Bain subdivided an area of land in North Coburg, calling the estate “Merlynston” after his daughter. The settlement grew as returned soldiers and other young people populated the area, leading to a call to Archbishop Harrington Lees for the provision of a place of worship for Church of England people. The Diocese agreed to purchase the land on which the present church stands together with the two adjoining blocks. In 1925 a church hall was built and was used as the worship centre until the actual church build could commence in 1931.
The architect Charles Heath, who designed the layout of the Fawkner Cemetery, had been chosen to design the St Linus church. He came up with a grand and architecturally impressive building, which, perhaps fortunately, was never completed in its original form.
The nave of St Linus' Church was built in 1932. It was planned as the first section of a most imposing building which, when complete, would have included transepts, a central tower and spire, and a sanctuary. These later sections were never completed.
A temporary wall was erected where the transepts were intended to be placed. It stayed for 46 years until the current east facing large glass window was constructed in 1978.