Polycystic ovarian syndrome (PCOS) is a common heterogeneous endocrine disease associated with a twofold higher risk of stroke and venous thromboembolism (VTE). An 18-year-old female presented to the emergency department (ED) with a one-hour history of right-side body weakness, facial asymmetry, and altered mental status. The patient had poor mentation and was unable to protect her airway. She was intubated and admitted to the intensive care unit (ICU). She was diagnosed with polycystic ovarian syndrome three years ago; however, she was not on active treatment at the time of presentation. She received two doses of the BNT162b2 mRNA COVID-19 vaccine, and her last dose was six months before the current presentation. A workup showed that she had extensive arterial and venous thrombosis. Later during investigations, she was found to have a complex atrial septal defect (ASD) with a left-to-right shunt. This case reports a management approach for a young female with untreated polycystic ovarian syndrome that predisposed her to develop deep vein thrombosis (DVT), pulmonary embolism (PE), and ischemic stroke due to atrial septal defect with possible transient shunt reversal.