The town was planned by the Western Australian Land Company, who built the Great Southern Railway in 1886-1889. It was originally known as Lakeside, due to its proximity to Lake Powell, but did not develop initially. The Government purchased the railway in 1896, redesigned the town and gazetted it as Lakeside in 1899. The town emerged as a railway junction between the Torbay line, which served timber sawmills in the area, and the Great Southern railway, and it was renamed Torbay Junction in 1908. In 1921, it was renamed Elleker on the recommendation of a former member of the Albany Road Board who lived in the area, after Ellerker in the East Riding of Yorkshire. The reasons for the omission of the first "r" are not known.
Elleker is the home of Severe Storms Research (SSR), a privately funded meteorological research facility specialising in the study of Deep, Moist, Convective events (Super Cell / Severe Thunderstorms) SSR operates a fully equipped mobile atmospheric observatory and a ground station. SSR also operates METREP (METeorological REPort), a significant weather event reporting system (similar to the BOM storm spotters program).
The townsite includes several houses, a general store, oval, town hall, railway siding as mentioned and a telephone booth.