Hayes has been a trailblazer for the women's game in English football since becoming Chelsea manager in 2012.
In more than a decade at the club, Hayes has led the Chelsea women's team to six Women's Super League titles, two Continental Cups, the Spring Series, a Community Shield victory and a Champions League final.
The 47-year-old intends to continue her career outside the Women's Super League and has been linked with the manager's job at the United States Women's national team.
Chelsea co-sporting directors Laurence Stewart and Paul Winstanley said: "Emma has been one of the biggest drivers of change in women's football. Her achievements at Chelsea are unrivalled and will live in the club's history forever.
"Given everything she has contributed to Chelsea in over a decade with the club, and the legacy she leaves behind, we would never stand in her way when she felt it was the right time to pursue a new challenge.
"We are pleased that she will remain with the club for the remainder of the season to give us the time to identify her successor.
"There will be plenty of time to celebrate Emma's many achievements at the club and to give her the farewell she deserves, but for now, as she always has been, Emma will be solely focused on making this season as successful as possible for Chelsea."
