When the Flügels folded in 1999, they supported the creation of Yokohama FC to replace them.

In 2012, they played Japan Football League for the first time and finished in 6th position.

After two seasons spent at JFL, YSCC Yokohama play in newly formed league, J3 from 2014.

On 7 December 2024, YSCC Yokohama secure relegation to Japan Football League after defeat from Kochi United SC 0-2 in 2nd leg of J3/JFL play-offs and lost aggregate 1-3, ended 11 years in third tier.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.