The club was founded as a football club of Yokogawa Electric Corporation in 1939. In 1978, the club achieved their first promotion to the Kanto Regional League. Despite experiencing the relegation to the Tokyo Prefecture League twice, they were determined to bounce back and gained the promotion to the Japan Football League in 1999. Although the club still have strong association with Yokogawa Electric, they left the nest in 2003 and started the new life as a non-corporation club under the name Yokogawa Musashino until 2015. The club was renamed Tokyo Musashino City in January 2016.
Their home ground is Musashino Municipal Athletic Stadium but they also play some of their home games at Ajinomoto Stadium, Ajinomoto Stadium sub ground, Edogawa Stadium, and Nishigaoka Soccer Stadium.