Endometriosis is a benign disease but with malignant behavior, sharing numerous features with cancers. Endometriosis is the development of endometrial tissue outside the uterus, with the presence of both glands and stroma. Approximately 10% of women of reproductive age suffer from endometriosis; it involves high social costs and affects the patient’s quality of life. In this review, we attempt to capture the pathogenesis mechanisms that are common to endometriosis and cancer based on molecular biology, focusing more on the principle of immunological changes and stemness. Clinical applicability will consist of targeted treatments that represent future directions in these diseases, which impose a burden on the healthcare system. Unlike endometriosis, cancer is a disease with fatal evolution, with conventional treatment based on chemo/radiotherapy. Here, we focus on the niche of personalized treatments that target molecular pathways. Our findings show that, in both pathologies, the resistance to treatments is due to the stemness of the stem cells, which might play a role in the appearance and evolution of both diseases. More research is needed before we can draw firm conclusions.