The club was founded in 1990 as Prima Aseno FC by the factory workers of Prima Ham (a food company) in Tsuchiura. It changed its name to Prima Ham FC Tsuchiura and gained promotion to the Japan Football League after finishing as runner-up in the 1996 Regional League play-off. It merged with FC Mito (founded in 1994) and re-branded itself as Mito HollyHock before the start of the 1997 season when Prima Ham decided to discontinue its financial support to the club.
Mito's application to play in the inaugural 1999 season of J. League Division 2 was initially turned down due to an unstable financial and fan base. However, after finishing 3rd in the Japan Football League in 1999 and gaining support, the club was invited into the J. League in 2000.
As of 2016, Mito HollyHock fields teams in women's football in Kanto league division 2, and ice hockey in the Ibaraki prefecture league.
Being a traditionally weak club in the league, Mito has tended to play a defensive game and has proven successful at it. This stinginess at the back is often referred to as "Mito-nachio" after the Catenaccio playing style, which is also a pun on the hometown's local specialty, Mito natto.
Recently, though, the team has been attempting implementation of stronger offensive tactics in an attempt to gain momentum for a promotion bid.