Since gaining J.League membership in 2001, Yokohama spent considerable time in the second tier of the Japanese football league system.

Instead, with money raised through donations from the general public and an affiliation with talent management company IMG, the former Flügels supporters founded the Yokohama Fulie Sports Club.

[1] For its first season in 1999, Yokohama hired former Germany national team and FIFA World Cup star Pierre Littbarski to be the manager and Yasuhiko Okudera, the first Japanese footballer to play professionally in Europe, to be the chairman.

Yokohama had lost all of their pre-season matches, including against college teams; they later hired player-manager Takuya Takagi, under whom they saw success.

Yokohama's financial situation remained poor, with no ownership of their stadium or training ground, and few staff members.

In 2007, just the ninth year of its existence, Yokohama played its first season in the top flight of Japanese football.

On 11 November 2024, Yokohama FC secure promotion again to J1 from 2025 after draw against Renofa Yamaguchi 0-0 in final matchweek and ended one year stint in second tier.

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

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