The current name combines two originally separate places. Withern shows the influence of Old Norse on an English place-name. Originally, this name was formed from the Old English elements widu ‘wood’ + ærn ‘a house’. However, given the large number of Scandinavian speakers in the area, they pronounced the first element as if it was the cognate Old Norse element viðr, also meaning ‘wood’. The ‘th’ in the modern form preserves this pronunciation difference between the closely-related Old English and Old Norse elements.

Stain comes directly from Old Norse steinn ‘stone’ – the place was presumably named after a prominent stone there. Many other place-names in Lincolnshire, like Stainby, Stainfield and Stainton, also contain this word as their first element. Elsewhere in England, such names tend to be spelled ‘Stan-‘, like the very common Stanton, which is the same name but deriving its first element from Old English stān ‘stone’.