Zephyr Junction evolved as a railroad town due to location of two railway systems that passed near Zephyr, Ontario.  They were the Lake Simcoe Junction Railway Company, established in 1877 and the Canadian Northern Railway, later the Grand Trunk Railway, established in 1906.

The Toronto & Nipissing Railway arrived in nearby Stouffville in 1871, to service the lumber industry, feeding markets like New York and Europe.  lumber and sawmill operations were located in adjacent towns, such as, Vandorf, Ballantrae and Zephyr.

Zephyr became a railroad town in 1877, as a result of the Lake Simcoe Junction Railway.  The first tracks were three miles to the west of the centre of town, with the first station erected in 1880 on the south side of the Zephyr side road.  Zephyr was essentially a flag-stop.