Ovarian ependymomas are extremely rare tumors of the ovary. We present a case of a 67-year-old lady presented to us with swelling in the right side of neck for 2 months followed by pelvic pain, lower abdominal distention, and weight loss for 1 month. Her coagulation profile, blood chemistry, lipid profile, and tumor markers were within normal limits. Neck Doppler ultrasonography revealed thrombus in the right internal jugular vein and CT scan of the abdomen showed bilateral ovarian masses. Patient was subjected to debulking surgery for suspected ovarian cancer and microscopy revealed a highly cellular tumor composed of small cells with hyperchromatic, round-to-oval nuclei with scanty cytoplasm, and perivascular pseudorosettes. Diagnosis was confirmed by immunophenotype showing strong positivity to glial fibrillary acidic protein, estrogen receptors, and progesterone receptors. Patient was successfully managed with anticoagulants, adjuvant chemotherapy with BEP regimen, and letrozole. After ruling out other common conditions for thrombosis in this age group, this seems to be a paraneoplastic presentation of ovarian malignancy that preceded the diagnosis of ependymoma by 2 months. To the best of our knowledge this is the first case report in the world literature as "paraneoplastic internal jugular vein thrombosis leading to diagnosis of bilateral ovarian ependymoma."