The condition occurs when tissue similar to the lining of the womb grows outside the uterus, which can have significant long-term impacts on health.
Hayes has now announced that she went for an emergency hysterectomy amid her "ongoing battle" last week, and she will be away from the touchline for the foreseeable future while she recovers.
"Last Tuesday I underwent an emergency hysterectomy following my ongoing battle with endometriosis. I'm now in recovery and will need time and patience to return to full health," Hays said in a statement on chelseafc.com.
"Throughout my absence, Denise Reddy will be making the on-field decisions along with Paul Green who will be carrying out all press obligations on my behalf.
'We have built a tremendous team over many years and we've adopted a very multi-disciplinary approach so that if situations like this arise, we are capable of being able to respond to the challenge. We have full confidence in Paul, Denise and all of the staff.
"We also know the team are very special and we have no doubt they'll do everything to maintain their high standards. To our fans, you've had to listen to me bellowing from the other side of the pitch every week but now I want to hear you even louder because I'll be sitting at home watching the team on the television until my return.
"I know you'll respect that my health comes first and at this time I've got to prioritise what I need to do for me. I fully expect to make a full recovery and I look forward to seeing you in the foreseeable future."
Chelsea sit fourth in the Women's Super League table after taking six points from their opening three games of the 2022-23 season and are next in action away to Everton on Sunday afternoon.