Post-COVID syndrome has an impact on women of reproductive age, causing menstrual cycle disorders that are pathophysiologically associated with the multisystem consequences of COVID-19, including endothelial dysfunction, microthrombosis, and neuroendocrine disturbances affecting the function of the hypothalamic-pituitary-gonadal and hypothalamic-pituitary-adrenal axes. Existing treatment protocols are primarily focused on classical causes such as hormonal imbalance and structural abnormalities, but they often fail to take into account the vascular, immune, and neuroendocrine mechanisms induced by SARS- CoV-2. The aim of our study was to evaluate the clinical efficacy and tolerability of a pathogenetically based modified therapy for menstrual cycle disorders in women after COVID-19 compared with standard treatment protocols. The study included 158 women of reproductive age with menstrual disorders in the post-COVID period. Patients of group 2 (n = 78) received treatment according to the Unified Clinical Protocols of the Ministry of Health of Ukraine, clinical guidelines, and international recommendations. Patients of group 1 (n = 80) received a modified comprehensive pathogenetic regimen that included hormonal, vascular- metabolic, neuroendocrine, and micronutrient support. Treatment schemes were adapted depending on the type of disorder (polymenorrhea, hypomenorrhea, menometrorrhagia, opsoligomenorrhea, secondary amenorrhea). According to the results of the study, the relapse rate after treatment in group 1 was significantly lower for all types of disorders: polymenorrhea – 13.3% vs. 73.3%, hypomenorrhea – 8.7% vs. 69.6%, opsoligomenorrhea – 16% vs. 56%, menometrorrhagia – 23.5% vs. 76.5%, amenorrhea – 20% vs. 80%. Complete normalization of menstrual fu nction was observed in 72–84% of women in the main group compared with 33–52% in the control group. A decrease in the need to modify the therapeutic regimen and a significant improvement in treatment tolerability were also recorded (P < 0.05). Pathogenetically based personalized therapy for menstrual cycle disorders in women after COVID-19 provides significantly better outcomes than standard protocols. Elimination of vascular, immune, and neuroendocrine consequences of COVID-19 is a key factor in the effective restoration of menstrual function in women of reproductive age with post-COVID menstrual disorders.