Yokogawa Musashino FC was originally established in 1939 as the club team of Yokogawa Electric, making it one of the oldest clubs in Japan. Based in Musashino City, in the western suburbs of Tokyo, Yokogawa entered the Kanto League during the 1970s with the formation of the Japan Soccer League. The team was quite competitive in the early years of the JSL, but following the formation of the J.League, Yokogawa Electric maintained a "company team" structure, and stayed in the amateur ranks, setting itself the goal of becoming one of the top amateur teams in the country. Since then, the team has gone through several incarnations, changing its name to Yokogawa FC and then to Yokogawa Musashino FC.

By the mid-90s, Yokogawa had become one of the strongest teams in the Kanto region, playing at the Regional level and winning the Kanto League title in both 1997 and 1998. With the formation of a J.League second division in 1999, Yokogawa FC became one of the most competitive clubs still in the amateur ranks, and was promoted to the newly reorganized JFL for the 1999 season. Since that time, the team's performance has been mediocre, but at least it seems to receive enough support from the corporate sponsor to be competitive. Support is steady, with attendances averaging a respectable 500 or so fans at home matches. In 2001 and 2002, the team finished seventh out of sixteen teams - their best result to date. Yokogawa FC changed its name to Yokogawa Musashino FC in 2002, in an effort to develop more of a grassroots image, and build a local fan base in the Musashino area, west of Tokyo. During the 2005 season, Yokogawa Musashino climbed as high as second place during the early part of the season, but a distinct lack of firepower combined with several catastrophic results such as a 2-1 defeat to bottom-of-the-table Mitsubishi Mizushima saw them drop into the lower half of the table by the end of the season, to finish in ninth place. Considering the steadily rising standard of competition in the JFL that has occurred, it will be something of a surprise if the team is able to match even that result, in 2006.