The physiology of reproduction is affected by psychological distress through neuroendocrine pathways. Historically, COVID-19 is one of the most stressful events with devastating consequences. This research aims to investigate the relationship between dysmenorrhea, PMS, and reproductive tract health on one hand, and COVID-19-related anxiety, depression, and stress on the other among medical students in Jordan. Medical students were invited through teaching platforms and social media to complete an online survey. SPSS software was used to analyze data. A total of 385 medical students participated in this research. Hence, 49.9% of the study population reported severe dysmenorrhea during COVID-19 compared to 36.9% before COVID-19 (p = 0.000). Dysmenorrhea was significantly associated with disruptions of sport and daily activities during COVID-19 (p = 0.015 and p = 0.002, respectively). The prevalence of PMS components, e.g., mastalgia, fatigue, headache, palpitation, and emotional and sleep disturbances, was raised during COVID-19 compared with before (p < 0.05). Symptoms of genitourinary tract infections, such as lower abdominal pain, vaginal discharge, genitalia rash/ulcers and itching, and urgency, were significantly increased after COVID-19 (p < 0.05). Positive Pearson correlations between COVID-19-associated mental health disorders and dysmenorrhea severity, PMS, and genital tract health abnormalities were observed (p < 0.05). The multiple linear regression model revealed that dysmenorrhea severity, PMS symptoms like palpitation, and genitourinary symptoms like lower abdominal pain and urgency were associated with worsening of depression, while dysuria was associated with a protective effect against depression. Moreover, it was observed that dysmenorrhea severity, PMS symptoms, such as headache and palpitation, and urinary urgency were associated with aggravation of anxiety. However, food craving and dysuria were protective against anxiety. Finally, dysmenorrhea severity, PMS symptoms of headache and palpitation, lower abdominal pain, and urgency were related to worsening of stress, whereas the premenstrual symptom of breast pain was a protective factor against stress. This work showed that COVID-19 pandemic-related psychological distress and menstrual, premenstrual, and genitourinary symptoms are closely related. Further future work is required to evaluate the long lasting-effects of the pandemic on mental health and the physiology of reproduction.