Endometriosis is a chronic disease, affecting approximately 10% of women of reproductive age. Ovarian endometriotic cysts or endometriomas are of particular relevance to fertility due to the negative impacts of both the disease and its treatment on prognosis. It is important for clinicians, especially those in non-fertility settings, to be aware of the evolving evidence and options for treatment in these women. The role of assisted reproduction techniques, prior to or alongside surgery need to be carefully considered. We outline an evidence-based framework to help facilitate fertility-friendly discussion, counseling and management of this complex disease.