Endometriosis and adenomyosis are debilitating gynecological conditions that severely affect the quality of life of women. Traditional diagnostic and treatment methods, including laparoscopic surgery and hormonal therapy, face significant limitations such as incomplete lesion detection, high recurrence rates, and adverse side effects. Emerging bioengineering technologies offer promising solutions for precise diagnosis and therapy of these diseases. Advances in biomarker detection through electrochemical immunosensors, including specific molecular markers like cytokines and growth factors, have improved their early diagnosis. Innovative imaging techniques, such as near-infrared fluorescence imaging, magnetic resonance imaging, and photoacoustic imaging, enhance lesion visualization and surgical precision. In therapeutic applications, bioengineered drug delivery systems enable targeted therapy by modifying drug carriers with ligands targeting highly expressed receptors in endometriotic lesions. Such strategies could improve drug accumulation at target sites and reduce damage to healthy tissues. Integrating external energy (including lasers, focused ultrasound, and magnetic fields) with nanoplatforms offers key benefits for treating endometriosis and adenomyosis, allowing precise delivery of energy-responsive molecules to lesions and minimizing damage to healthy tissues. Additionally, novel approaches, such as immunotherapy, gene therapy, ferroptosis induction, and synthetic lethal activation, offer new avenues for effective treatment of endometriosis and adenomyosis. Significantly, this paper discusses the advantages of precision diagnosis and treatment of endometriosis in preserving the fertility of women of reproductive age. This review highlights the potential of bioengineering breakthroughs to transform the diagnosis and management of endometriosis and adenomyosis, emphasizing their role in advancing precision medicine and improving women's health.