It was named for Captain C. H. Bagot, who owned a great deal of property in the area.

On 16 March 2000, boundaries for the locality were created for the "long established name.

"[6][3] Bagot Well was served by the Morgan railway line from when it was extended from Kapunda in 1878.

The line was closed in 1994, but passenger services had ceased much earlier and freight trains carrying bulk grain from Eudunda to Port Adelaide did not stop there.

The 2016 Australian census which was conducted in August 2016 reports that Bagot Well had a population of 84 people.