The senior side initially played in the Victorian Amateur Football Association before deciding to join the same competition their juniors participated in so they transferred in from the VAFA.
Rupertswood had for years competed in the junior competitions with the Riddell District Football League. Rupertswood seniors joined in full in 2013. It had been fielding juniors for some years. The senior side transferred in from the VAFA.
In 2021, Rupertswood transferred to the EDFL Division 1.