The 48-year-old Kimura will remain at the helm until the fourth round of the Emperor's Cup on Nov. 15. No one has been named yet to replace him.
Kimura took over from Takashi Kuwahara after 17 games last season and helped guide the team from 16th place to ninth with an 8-4 record, with six draws.
This season, however, Yokohama have struggled to gain points sinceom the beginning of the season and have a 10-9 record with 11 draws and linger in 10th place.