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Purpose To report a rare case of bilateral pulmonary emboli following pars plana vitrectomy with postoperative prone positioning. Observations A 60 year-old female presented with a fourmonth history of unilateral distorted vision. Ocular coherence tomography revealed a full thickness macular hole. Two weeks later, the patient underwent a 23-gauge pars plana vitrectomy with internal limiting membrane peeling and 12% perfluoropropane gas tamponade. Postoperatively, she completed two weeks of prone positioning. Five days later, she presented with a two day history of abdominal pain and shortness of breath. Computed tomography angiography revealed bilateral pulmonary emboli. The patient received six months of anticoagulation to prevent further thromboembolic events. Conclusions Life threatening blood clots can form due to prolonged immobilization from prone positioning. Patients should be educated to perform light exercise postoperatively to prevent complications of blood stasis.