The club entered the VFL in 1998 as the Bendigo Diggers and then, in 2003, formed an alliance with the Essendon Football Club in the Australian Football League which results in Essendon being able to also field some players in the Bendigo team and gaining a supporter base in the large regional city. Essendon re-aligned with the Bendigo Bombers in late 2009 for a further two seasons.
The Diggers moniker was changed to the Bendigo Bombers in the same year to reflect the moniker of the Essendon AFL club.